Variant report

Variant	rs16891458
Chromosome Location	chr6:26234476-26234477
allele	A/C
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26233448..26235462-chr6:27099272..27101626,2	MCF-7	breast:
2	chr16:33963952..33966447-chr6:26233532..26235518,2	MCF-7	breast:
3	chr6:26233018..26235518-chr6:27781228..27784528,3	MCF-7	breast:
4	chr13:108869881..108870622-chr6:26234047..26234816,2	NB4	blood:
5	chr6:26031185..26034143-chr6:26233658..26236359,2	MCF-7	breast:
6	chr21:44526126..44528705-chr6:26232568..26234835,2	MCF-7	breast:
7	chr6:26232392..26235722-chr6:27100798..27102386,3	K562	blood:
8	chr6:26231234..26236589-chr6:27099738..27104932,8	K562	blood:
9	chr17:56736343..56738004-chr6:26233634..26236262,2	MCF-7	breast:
10	chr6:26020523..26023508-chr6:26233779..26236758,2	MCF-7	breast:
11	chr6:26225643..26226465-chr6:26234066..26234965,2	MCF-7	breast:
12	chr15:74753352..74756015-chr6:26233514..26236458,2	K562	blood:
13	chr6:26233781..26236628-chr6:27113286..27115220,2	K562	blood:
14	chr16:2009340..2011468-chr6:26233811..26235989,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000247240	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000200434	Chromatin interaction
ENSG00000160201	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000138629	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000182611	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000140990	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000184825	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1000308	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs10484437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341758	1.00[ASW][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16891404	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16891417	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16891421	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891440	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891450	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891453	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891471	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891477	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16891497	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs16891501	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs16891505	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17533076	1.00[ASW][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17598764	0.82[EUR][1000 genomes]
rs17598927	1.00[ASW][hapmap]
rs17600910	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs34550794	1.00[ASW][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3818947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41266803	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41266805	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4593350	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55856153	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56360223	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56372675	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61910695	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6913828	0.89[CEU][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs989710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv1021294	chr6:26190316-26246784	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	309 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16891458	HIST1H1D	cis	Liver	GTEx
rs16891458	HIST1H2AE	cis	lymphoblastoid	seeQTL
rs16891458	HIST1H1D	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26231200-26236000	Active TSS	Thymus	Thymus
2	chr6:26232400-26236000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:26232600-26234800	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr6:26232600-26235800	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:26232800-26234800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:26232800-26234800	Flanking Active TSS	K562	blood
7	chr6:26232800-26235000	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr6:26232800-26235000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:26232800-26235400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:26232800-26235600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:26232800-26235600	Active TSS	Aorta	Aorta
12	chr6:26232800-26235800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:26232800-26235800	Active TSS	Fetal Lung	lung
14	chr6:26233000-26235000	Flanking Active TSS	Dnd41	blood
15	chr6:26233000-26235400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:26233000-26235600	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr6:26233000-26235800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr6:26233000-26235800	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr6:26233000-26235800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
20	chr6:26233000-26236000	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr6:26233000-26236000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:26233200-26234800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:26233200-26235000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:26233200-26235200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:26233200-26235200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:26233200-26235200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr6:26233200-26235200	Flanking Active TSS	Placenta	Placenta
28	chr6:26233200-26235200	Active TSS	Small Intestine	intestine
29	chr6:26233200-26235400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:26233200-26235400	Active TSS	Esophagus	oesophagus
31	chr6:26233200-26235400	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr6:26233200-26235400	Transcr. at gene 5' and 3'	Right Atrium	heart
33	chr6:26233200-26235600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:26233200-26235600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr6:26233200-26235600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
36	chr6:26233200-26235600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
37	chr6:26233200-26235600	Bivalent/Poised TSS	Psoas Muscle	Psoas
38	chr6:26233200-26235800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr6:26233200-26235800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr6:26233200-26235800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:26233200-26235800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:26233200-26235800	Active TSS	Fetal Stomach	stomach
43	chr6:26233200-26235800	Active TSS	Rectal Smooth Muscle	rectum
44	chr6:26233200-26235800	Flanking Active TSS	HUVEC	blood vessel
45	chr6:26233200-26235800	Active TSS	NHLF	lung
46	chr6:26233200-26236000	Active TSS	Fetal Kidney	kidney
47	chr6:26233200-26236000	Active TSS	A549	lung
48	chr6:26233400-26235200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr6:26233400-26235400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:26233400-26235600	Active TSS	iPS-18 Cell Line	embryonic stem cell

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