Variant report

Variant	rs129128
Chromosome Location	chr6:26125342-26125343
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:143)
CpG islands
(count:0)
Chromatin interactive
region (count:38)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:143 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr6:26122615-26125565	GM12878	blood:	n/a	n/a
2	USF2	chr6:26124506-26125439	K562	blood:	n/a	n/a
3	MYBL2	chr6:26125217-26127041	HepG2	liver:	n/a	n/a
4	MXI1	chr6:26122292-26127660	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr6:26122842-26126800	U87	brain:	n/a	n/a
6	MBD4	chr6:26123812-26125542	HepG2	liver:	n/a	n/a
7	TCF12	chr6:26122459-26125586	A549	lung:	n/a	chr6:26125022-26125029
8	PML	chr6:26122751-26126510	GM12878	blood:	n/a	n/a
9	CREB1	chr6:26125297-26127115	K562	blood:	n/a	n/a
10	POLR2A	chr6:26122292-26127005	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:26123011-26125353	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:26122637-26126581	HepG2	liver:	n/a	n/a
13	MXI1	chr6:26124977-26125602	K562	blood:	n/a	n/a
14	POLR2A	chr6:26122768-26126187	GM12891	blood:	n/a	n/a
15	POLR2A	chr6:26122490-26127190	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr6:26123103-26125906	GM18951	blood:	n/a	n/a
17	JUND	chr6:26122801-26125545	HCT-116	colon:	n/a	n/a
18	POLR2A	chr6:26122754-26125554	HUVEC	blood vessel:	n/a	n/a
19	ETS1	chr6:26122979-26125371	A549	lung:	n/a	n/a
20	POLR2A	chr6:26122721-26126760	HepG2	liver:	n/a	n/a
21	POLR2A	chr6:26122233-26126588	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr6:26122645-26126677	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr6:26123126-26126759	HL-60	blood:	n/a	n/a
24	NR2F2	chr6:26122671-26125498	K562	blood:	n/a	n/a
25	POLR2A	chr6:26122651-26126425	GM12878	blood:	n/a	n/a
26	STAT5A	chr6:26122847-26125675	GM12878	blood:	n/a	chr6:26124082-26124106
27	POLR2A	chr6:26122667-26126786	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr6:26122407-26127601	SK-N-MC	brain:	n/a	n/a
29	POLR2A	chr6:26122661-26125348	HepG2	liver:	n/a	n/a
30	POLR2A	chr6:26123039-26125488	NB4	blood:	n/a	n/a
31	PML	chr6:26122206-26129108	K562	blood:	n/a	n/a
32	POLR2A	chr6:26122631-26127062	PFSK-1	brain:	n/a	n/a
33	POLR2A	chr6:26122640-26125897	K562	blood:	n/a	n/a
34	POLR2A	chr6:26112014-26135800	K562	blood:	n/a	n/a
35	CHD2	chr6:26122727-26125578	K562	blood:	n/a	n/a
36	CHD1	chr6:26122945-26127005	H1-hESC	embryonic stem cell:	n/a	n/a
37	SIN3AK20	chr6:26122600-26127033	MCF-7	breast:	n/a	n/a
38	SIN3A	chr6:26123899-26125361	GM12878	blood:	n/a	n/a
39	POLR2A	chr6:26122660-26127109	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr6:26125147-26126651	ECC-1	luminal epithelium:	n/a	n/a
41	FOXM1	chr6:26122719-26125478	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:26122630-26125525	K562	blood:	n/a	n/a
43	POLR2A	chr6:26122676-26125938	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr6:26122687-26126019	HCT-116	colon:	n/a	n/a
45	POLR2A	chr6:26122613-26126646	GM12892	blood:	n/a	n/a
46	TBL1XR1	chr6:26122733-26125585	K562	blood:	n/a	n/a
47	POLR2A	chr6:26122693-26126578	GM12891	blood:	n/a	n/a
48	POLR2A	chr6:26122626-26127189	Hela-S3	cervix:	n/a	n/a
49	ATF2	chr6:26122582-26127052	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr6:26122901-26126794	U87	brain:	n/a	n/a

No data

(count:38 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26122965..26125832-chr6:27791721..27793805,2	K562	blood:
2	chr1:45239970..45242473-chr6:26124301..26126003,2	K562	blood:
3	chr6:26043872..26047495-chr6:26122651..26127553,11	MCF-7	breast:
4	chr6:26121366..26126112-chr6:27111465..27116295,14	K562	blood:
5	chr19:3976743..3979264-chr6:26123642..26125833,2	K562	blood:
6	chr6:26123945..26125914-chr6:26596676..26599538,2	MCF-7	breast:
7	chr6:26120836..26126141-chr6:27110374..27116911,13	K562	blood:
8	chr10:103576855..103578290-chr6:26124281..26125400,4	Hela-S3	cervix:
9	chr6:26122455..26127911-chr6:27777953..27784057,9	MCF-7	breast:
10	chr6:26124249..26127079-chr6:27774998..27777814,2	MCF-7	breast:
11	chr6:26124491..26125367-chr6:26157372..26158307,5	MCF-7	breast:
12	chr6:26123458..26125812-chr6:27833699..27835902,2	K562	blood:
13	chr6:26123030..26125902-chr6:43596197..43598977,2	MCF-7	breast:
14	chr6:26123538..26126463-chr6:27839841..27841380,2	MCF-7	breast:
15	chr6:26119257..26128074-chr6:27097161..27104707,27	K562	blood:
16	chr6:26124863..26126579-chr6:27106441..27107960,2	K562	blood:
17	chr6:26122616..26125832-chr6:27791584..27793805,3	K562	blood:
18	chr6:25726417..25728737-chr6:26124112..26125886,2	K562	blood:
19	chr6:26119863..26128842-chr6:27096583..27102911,26	K562	blood:
20	chr18:12947366..12948044-chr6:26124586..26125548,2	Hela-S3	cervix:
21	chr6:26124612..26126281-chr6:27113113..27115082,2	MCF-7	breast:
22	chr15:72497728..72499574-chr6:26124420..26126089,2	MCF-7	breast:
23	chr6:26122811..26125684-chr6:26519933..26522732,4	K562	blood:
24	chr6:26017750..26036418-chr6:26116875..26130553,65	MCF-7	breast:
25	chr6:26124251..26127166-chr6:31695138..31698033,2	K562	blood:
26	chr2:11678697..11680691-chr6:26124783..26126367,2	MCF-7	breast:
27	chr6:26123627..26126510-chr6:42712308..42715108,2	MCF-7	breast:
28	chr20:45985883..45988402-chr6:26124998..26126661,2	MCF-7	breast:
29	chr6:26053512..26063692-chr6:26116837..26127451,29	MCF-7	breast:
30	chr6:26124860..26126999-chr6:27103096..27105177,2	MCF-7	breast:
31	chr3:49760150..49762136-chr6:26123661..26125632,2	K562	blood:
32	chr6:26121790..26128581-chr6:27110404..27116881,10	MCF-7	breast:
33	chr6:26121882..26125935-chr6:27097712..27102367,10	MCF-7	breast:
34	chr6:26124485..26126555-chr6:28456975..28458893,2	K562	blood:
35	chr6:26123459..26125455-chr6:27834569..27837416,2	MCF-7	breast:
36	chr1:149857091..149860702-chr6:26123340..26126187,3	MCF-7	breast:
37	chr6:26122693..26125810-chr6:27099221..27102076,5	MCF-7	breast:
38	chr14:31495982..31496780-chr6:26124834..26125403,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
HIST1H2BC	TF binding region
ENSG00000197903	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000198408	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000124688	Chromatin interaction
ENSG00000172432	Chromatin interaction
ENSG00000164508	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000167658	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000182611	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000124659	Chromatin interaction
ENSG00000197238	Chromatin interaction
ENSG00000196226	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000124610	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000173540	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000146047	Chromatin interaction
ENSG00000182572	Chromatin interaction
ENSG00000067225	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000198558	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000234816	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000213722	Chromatin interaction
ENSG00000184357	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1799945	0.87[AMR][1000 genomes]
rs198805	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs198812	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198833	1.00[ASN][1000 genomes]
rs198846	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs198851	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2032451	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs129128	FKSG83	cis	parietal	SCAN
rs129128	HIST1H3E	cis	parietal	SCAN
rs129128	HFE	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26121800-26125400	Active TSS	K562	blood
2	chr6:26122400-26127800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:26122600-26126800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:26122600-26127000	Active TSS	Brain Angular Gyrus	brain
5	chr6:26122600-26127000	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr6:26122600-26127000	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr6:26122600-26127200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:26122600-26127200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:26122600-26127200	Active TSS	Fetal Kidney	kidney
10	chr6:26122600-26127400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:26122600-26127600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:26122600-26127600	Active TSS	Brain Substantia Nigra	brain
13	chr6:26122600-26127800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:26122600-26127800	Active TSS	Psoas Muscle	Psoas
15	chr6:26122600-26128400	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr6:26122800-26126800	Active TSS	Placenta	Placenta
17	chr6:26122800-26126800	Active TSS	Rectal Smooth Muscle	rectum
18	chr6:26122800-26127000	Active TSS	Duodenum Mucosa	Duodenum
19	chr6:26122800-26127000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr6:26122800-26127200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:26122800-26127200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:26122800-26127200	Active TSS	Esophagus	oesophagus
23	chr6:26122800-26127200	Active TSS	Fetal Muscle Trunk	muscle
24	chr6:26122800-26127200	Active TSS	Left Ventricle	heart
25	chr6:26122800-26127200	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr6:26122800-26127200	Active TSS	Small Intestine	intestine
27	chr6:26122800-26127600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr6:26122800-26127600	Active TSS	Colonic Mucosa	Colon
29	chr6:26122800-26127600	Active TSS	Right Ventricle	heart
30	chr6:26122800-26128600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:26123000-26126000	Active TSS	HUVEC	blood vessel
32	chr6:26123000-26126200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr6:26123000-26126600	Active TSS	Primary T cells from cord blood	blood
34	chr6:26123000-26126600	Active TSS	Fetal Stomach	stomach
35	chr6:26123000-26126800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:26123000-26126800	Active TSS	Fetal Muscle Leg	muscle
37	chr6:26123000-26126800	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr6:26123000-26126800	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr6:26123000-26126800	Active TSS	Stomach Smooth Muscle	stomach
40	chr6:26123000-26127000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:26123000-26127000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:26123000-26127000	Active TSS	Brain Anterior Caudate	brain
43	chr6:26123000-26127000	Active TSS	Pancreas	Pancrea
44	chr6:26123000-26127000	Active TSS	Stomach Mucosa	stomach
45	chr6:26123000-26127200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:26123000-26127200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:26123000-26127200	Active TSS	Colon Smooth Muscle	Colon
48	chr6:26123000-26127200	Active TSS	GM12878-XiMat	blood
49	chr6:26123000-26127400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:26123000-26127400	Active TSS	Fetal Intestine Small	intestine

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