Variant report

Variant	rs1009181
Chromosome Location	chr6:26158993-26158994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:75)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:75 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr6:26157915..26159076-chr9:131314410..131315769,4	Hela-S3	cervix:
2	chr19:1438486..1441264-chr6:26157588..26160281,2	K562	blood:
3	chr20:45981040..45982698-chr6:26158330..26160765,2	MCF-7	breast:
4	chr6:26158231..26160273-chr6:26456660..26458707,2	K562	blood:
5	chr17:56736342..56737984-chr6:26158889..26160717,2	MCF-7	breast:
6	chr15:80351279..80352456-chr6:26158321..26159028,3	Hela-S3	cervix:
7	chr6:26158344..26159047-chr6:26199394..26200119,2	NB4	blood:
8	chr6:26158796..26160362-chr6:28889736..28891430,2	MCF-7	breast:
9	chr6:26154851..26161490-chr6:27803982..27809302,10	MCF-7	breast:
10	chr6:26157128..26159753-chr6:26519202..26521718,3	K562	blood:
11	chr6:26155821..26161666-chr6:26595746..26599191,6	K562	blood:
12	chr4:129731326..129732115-chr6:26158771..26159658,2	Hela-S3	cervix:
13	chr6:26158302..26159117-chr6:27775211..27776028,3	Hela-S3	cervix:
14	chr1:113161705..113162355-chr6:26158558..26159489,2	Hela-S3	cervix:
15	chr6:7541573..7543305-chr6:26157976..26160637,2	MCF-7	breast:
16	chr6:26157754..26159719-chrX:40035587..40037677,2	K562	blood:
17	chr11:62553654..62556441-chr6:26158091..26159898,2	MCF-7	breast:
18	chr17:39844898..39846717-chr6:26157632..26159911,2	MCF-7	breast:
19	chr6:26158606..26161579-chr6:26427700..26429391,2	K562	blood:
20	chr5:32767867..32768442-chr6:26158446..26159132,2	Hela-S3	cervix:
21	chr1:151583782..151586135-chr6:26156499..26159013,2	MCF-7	breast:
22	chr4:84205500..84206046-chr6:26158335..26159311,2	Hela-S3	cervix:
23	chr17:57917729..57920994-chr6:26157290..26159599,3	MCF-7	breast:
24	chr17:79476638..79478396-chr6:26156378..26158994,2	K562	blood:
25	chr6:26157950..26159489-chr6:26216516..26217479,4	Hela-S3	cervix:
26	chr6:26156242..26159092-chr6:26536120..26538666,4	K562	blood:
27	chr6:26158579..26159282-chr9:130565172..130565931,2	Hela-S3	cervix:
28	chr1:45987981..45988909-chr6:26158472..26159117,2	Hela-S3	cervix:
29	chr6:26156242..26159105-chr6:26536923..26540101,4	K562	blood:
30	chr4:74961279..74961967-chr6:26158517..26159473,2	Hela-S3	cervix:
31	chr6:26156539..26159752-chr6:27789792..27793850,5	MCF-7	breast:
32	chr6:26157049..26158999-chr6:26401561..26403598,2	K562	blood:
33	chr3:196294148..196296034-chr6:26157528..26159567,2	MCF-7	breast:
34	chr6:26041051..26050922-chr6:26154916..26161227,19	MCF-7	breast:
35	chr6:26158163..26159015-chr6:26183506..26184251,2	MCF-7	breast:
36	chr17:41116159..41116765-chr6:26158257..26159199,2	Hela-S3	cervix:
37	chr6:26156157..26159561-chr6:27098059..27103137,9	MCF-7	breast:
38	chr19:55896889..55897506-chr6:26158228..26159085,2	HCT-116	colon:
39	chr6:26156657..26159297-chr6:27111666..27115480,6	MCF-7	breast:
40	chr12:51157529..51159205-chr6:26158256..26159760,2	MCF-7	breast:
41	chr3:119812836..119813521-chr6:26158734..26159317,2	Hela-S3	cervix:
42	chr10:16478865..16480731-chr6:26157879..26159983,2	MCF-7	breast:
43	chr6:26154955..26159424-chr6:27857638..27862895,13	MCF-7	breast:
44	chr6:26158395..26159375-chr7:100026037..100026741,2	NB4	blood:
45	chr13:45010512..45011337-chr6:26158445..26159009,2	Hela-S3	cervix:
46	chr6:26154897..26160424-chr6:27112363..27117818,13	MCF-7	breast:
47	chr6:26155265..26160650-chr6:27098824..27104648,17	MCF-7	breast:
48	chr20:26188947..26190833-chr6:26156720..26159562,2	MCF-7	breast:
49	chr6:26158181..26160251-chr7:139476447..139479207,2	K562	blood:
50	chr6:26155301..26160613-chr6:27781458..27785146,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101040	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000059377	Chromatin interaction
ENSG00000233396	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000063046	Chromatin interaction
ENSG00000268798	Chromatin interaction
ENSG00000243789	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000086666	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000102804	Chromatin interaction
ENSG00000228395	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000185475	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000231119	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000115268	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000064393	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000233056	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000184348	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000072401	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000182611	Chromatin interaction
ENSG00000174013	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000198931	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000266967	Chromatin interaction
ENSG00000185798	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000197238	Chromatin interaction
ENSG00000269176	Chromatin interaction
ENSG00000168970	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000082996	Chromatin interaction
ENSG00000113240	Chromatin interaction
ENSG00000197694	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000250734	Chromatin interaction
ENSG00000199289	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000082701	Chromatin interaction
ENSG00000197697	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000234816	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000183337	Chromatin interaction
ENSG00000131653	Chromatin interaction
ENSG00000173085	Chromatin interaction
ENSG00000026950	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000260260	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000266077	Chromatin interaction
ENSG00000227195	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000136877	Chromatin interaction
ENSG00000096696	Chromatin interaction
ENSG00000181788	Chromatin interaction
ENSG00000066135	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000226645	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000112763	Chromatin interaction
ENSG00000165983	Chromatin interaction
ENSG00000196226	Chromatin interaction
ENSG00000096654	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1059490	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2066295	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2183947	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4486004	0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6906367	0.80[YRI][hapmap]
rs806973	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9366639	0.89[CHD][hapmap]
rs9379827	0.89[CHD][hapmap]
rs9379828	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9379829	0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
8	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
9	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
10	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
11	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
12	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
13	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
14	nsv1025493	chr6:26026870-26223838	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1001 gene(s)	inside rSNPs	diseases
15	nsv1023979	chr6:26026870-26287399	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1113 gene(s)	inside rSNPs	diseases
16	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
17	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
18	nsv482348	chr6:26082709-26261136	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	799 gene(s)	inside rSNPs	diseases
19	nsv518431	chr6:26148311-26211368	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	521 gene(s)	inside rSNPs	diseases
20	nsv526456	chr6:26148311-26211368	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	521 gene(s)	inside rSNPs	diseases
21	nsv970083	chr6:26158290-26159152	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	239 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1009181	GMNN	cis	parietal	SCAN
rs1009181	HIST1H2BD	cis	lymphoblastoid	seeQTL
rs1009181	HIST1H3G	cis	cerebellum	SCAN
rs1009181	BTN3A2	cis	multi-tissue	Pritchard
rs1009181	HIST1H2BD	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26155400-26160800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:26155600-26159600	Active TSS	Fetal Lung	lung
3	chr6:26155600-26159600	Active TSS	Psoas Muscle	Psoas
4	chr6:26155600-26159800	Active TSS	Fetal Kidney	kidney
5	chr6:26155600-26159800	Active TSS	HSMMtube	muscle
6	chr6:26155600-26160000	Active TSS	Brain Cingulate Gyrus	brain
7	chr6:26155600-26160600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:26155600-26160800	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:26155800-26159600	Active TSS	Colon Smooth Muscle	Colon
10	chr6:26155800-26159600	Active TSS	Right Ventricle	heart
11	chr6:26155800-26159600	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr6:26155800-26159800	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr6:26155800-26159800	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr6:26155800-26160000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:26155800-26160000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:26155800-26160000	Active TSS	Placenta Amnion	Placenta Amnion
17	chr6:26155800-26160200	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr6:26155800-26160200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:26155800-26160200	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr6:26155800-26160200	Active TSS	Fetal Intestine Large	intestine
21	chr6:26155800-26160200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr6:26155800-26160200	Active TSS	A549	lung
23	chr6:26155800-26160200	Active TSS	HSMM	muscle
24	chr6:26155800-26160400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr6:26155800-26160400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:26155800-26160400	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:26155800-26160400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:26155800-26160400	Active TSS	Pancreas	Pancrea
29	chr6:26155800-26160600	Active TSS	H1 Cell Line	embryonic stem cell
30	chr6:26155800-26160600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:26155800-26160600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:26155800-26160600	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr6:26155800-26160800	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr6:26155800-26160800	Active TSS	Colonic Mucosa	Colon
35	chr6:26155800-26161200	Active TSS	Thymus	Thymus
36	chr6:26156000-26159000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:26156000-26159600	Active TSS	Left Ventricle	heart
38	chr6:26156000-26159600	Active TSS	Rectal Smooth Muscle	rectum
39	chr6:26156000-26159800	Active TSS	Primary B cells from peripheral blood	blood
40	chr6:26156000-26159800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:26156000-26159800	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr6:26156000-26159800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:26156000-26159800	Active TSS	Brain Anterior Caudate	brain
44	chr6:26156000-26159800	Active TSS	HMEC	breast
45	chr6:26156000-26160000	Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr6:26156000-26160000	Active TSS	Stomach Mucosa	stomach
47	chr6:26156000-26160200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:26156000-26160200	Active TSS	Brain Substantia Nigra	brain
49	chr6:26156000-26160200	Active TSS	Esophagus	oesophagus
50	chr6:26156000-26160200	Active TSS	NHLF	lung

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