Variant report

Variant	rs16891512
Chromosome Location	chr6:26270609-26270610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:114)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:114 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:26270354-26274437	Raji	blood:	n/a	n/a
2	POLR2A	chr6:26270245-26271789	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:26266613-26275023	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:26269948-26272086	HUVEC	blood vessel:	n/a	n/a
5	CHD1	chr6:26270342-26274429	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:26269900-26271927	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr6:26270577-26270646	MCF-7	breast:	n/a	n/a
8	NFATC1	chr6:26270054-26271865	GM12878	blood:	n/a	n/a
9	CHD1	chr6:26269438-26274500	H1-hESC	embryonic stem cell:	n/a	n/a
10	POU2F2	chr6:26270319-26271773	GM12878	blood:	n/a	n/a
11	RCOR1	chr6:26270357-26273588	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr6:26268846-26274052	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr6:26269656-26274808	H1-hESC	embryonic stem cell:	n/a	n/a
14	PBX3	chr6:26270584-26270890	GM12878	blood:	n/a	n/a
15	WRNIP1	chr6:26270473-26270749	GM12878	blood:	n/a	n/a
16	MXI1	chr6:26270461-26272258	IMR90	lung:	n/a	n/a
17	POLR2A	chr6:26269878-26271808	IMR90	lung:	n/a	n/a
18	BCLAF1	chr6:26270286-26271762	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:26269993-26272096	GM18951	blood:	n/a	n/a
20	RELA	chr6:26270357-26272468	GM10847	blood:	n/a	n/a
21	POLR2A	chr6:26268932-26272051	GM12878	blood:	n/a	n/a
22	TCF7L2	chr6:26270512-26271843	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr6:26269717-26272823	GM12878	blood:	n/a	n/a
24	CEBPB	chr6:26270339-26272201	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:26269656-26271993	U87	brain:	n/a	n/a
26	POLR2A	chr6:26269658-26272205	GM12892	blood:	n/a	n/a
27	POLR2A	chr6:26269040-26274454	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr6:26270121-26271828	GM15510	blood:	n/a	n/a
29	PML	chr6:26269974-26272590	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:26269060-26272781	Hela-S3	cervix:	n/a	n/a
31	POU2F2	chr6:26270058-26272094	GM12878	blood:	n/a	n/a
32	RELA	chr6:26270371-26272188	GM19099	blood:	n/a	n/a
33	POLR2A	chr6:26270067-26272713	GM12891	blood:	n/a	n/a
34	MTA3	chr6:26269886-26274743	GM12878	blood:	n/a	n/a
35	SIN3AK20	chr6:26270143-26273935	MCF-7	breast:	n/a	n/a
36	POLR2A	chr6:26269097-26271768	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr6:26270373-26270819	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr6:26270133-26271796	GM12878	blood:	n/a	n/a
39	POLR2A	chr6:26270217-26272109	GM12891	blood:	n/a	n/a
40	POLR2A	chr6:26269678-26271833	U87	brain:	n/a	n/a
41	RUNX3	chr6:26270313-26271777	GM12878	blood:	n/a	n/a
42	ZKSCAN1	chr6:26270490-26272111	Hela-S3	cervix:	n/a	n/a
43	ETS1	chr6:26270326-26271743	GM12878	blood:	n/a	n/a
44	RELA	chr6:26270110-26272184	GM18505	blood:	n/a	n/a
45	ATF2	chr6:26270356-26271796	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:26269751-26271936	HUVEC	blood vessel:	n/a	n/a
47	ZBTB33	chr6:26270236-26272259	SK-N-SH	brain:	n/a	n/a
48	POU2F2	chr6:26270400-26270703	GM12891	blood:	n/a	n/a
49	RUNX3	chr6:26270254-26272035	GM12878	blood:	n/a	n/a
50	TAF7	chr6:26268962-26274860	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26270106..26271660-chr6:27833787..27835479,2	MCF-7	breast:
2	chr6:26270251..26272974-chr6:27776913..27779571,3	MCF-7	breast:
3	chr6:26270357..26275628-chr6:27773210..27778290,5	MCF-7	breast:
4	chr5:110077153..110078892-chr6:26269721..26271501,2	MCF-7	breast:
5	chr6:26270164..26274435-chr6:27112425..27114820,4	MCF-7	breast:
6	chr16:30075607..30076204-chr6:26270077..26270845,2	Hela-S3	cervix:
7	chr6:26270273..26274919-chr6:27857077..27861037,6	MCF-7	breast:
8	chr6:26268562..26271550-chr6:27838233..27840069,2	MCF-7	breast:
9	chr20:45945754..45947886-chr6:26270266..26272050,2	MCF-7	breast:
10	chr6:26268712..26271110-chr7:104650845..104653743,2	MCF-7	breast:
11	chr6:26270115..26271015-chr6:159238533..159239442,2	Hela-S3	cervix:
12	chr16:54319723..54320248-chr6:26270491..26271251,2	Hela-S3	cervix:
13	chr6:26269718..26276565-chr6:27099393..27105112,10	MCF-7	breast:
14	chr6:26026863..26028475-chr6:26270245..26272373,2	MCF-7	breast:
15	chr12:33049338..33049847-chr6:26270590..26271525,2	Hela-S3	cervix:
16	chr17:56736093..56737648-chr6:26268558..26271490,2	MCF-7	breast:
17	chr17:39845133..39845644-chr6:26270549..26271212,2	Hela-S3	cervix:
18	chr20:30310395..30311069-chr6:26270214..26271089,2	Hela-S3	cervix:
19	chr17:58602525..58604576-chr6:26270292..26271917,2	MCF-7	breast:

No data

Variant related genes	Relation type
HIST1H2BI	TF binding region
ENSG00000173812	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000233893	Chromatin interaction
ENSG00000149925	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000092820	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000057294	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000267882	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000171552	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000177508	Chromatin interaction
ENSG00000062725	Chromatin interaction
ENSG00000184357	Chromatin interaction
ENSG00000259349	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000164209	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10484437	0.85[MKK][hapmap]
rs1341758	0.96[MKK][hapmap]
rs16891417	0.96[MKK][hapmap]
rs16891509	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16891517	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16891518	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16891549	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17533076	0.96[MKK][hapmap]
rs17600910	0.82[CHB][hapmap];0.91[MKK][hapmap]
rs1883212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34550794	0.96[MKK][hapmap]
rs3778278	0.82[CHB][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41266827	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7450543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9366639	0.87[MKK][hapmap]
rs9379827	0.91[MKK][hapmap]
rs9379829	0.91[MKK][hapmap]
rs989710	0.96[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	184 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16891512	HIST1H2BG	cis	multi-tissue	Pritchard

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26252400-26271200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:26253800-26271000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:26266000-26271200	Weak transcription	Right Atrium	heart
4	chr6:26267400-26270800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:26269000-26274200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:26269000-26274800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:26269200-26273200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:26269200-26274600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr6:26269200-26274600	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr6:26269400-26271200	Weak transcription	Lung	lung
11	chr6:26269400-26272000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:26269400-26272200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:26269400-26273400	Active TSS	Hela-S3	cervix
14	chr6:26269400-26274400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr6:26269400-26274400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr6:26269400-26274800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr6:26269400-26275000	Active TSS	H1 Cell Line	embryonic stem cell
18	chr6:26269600-26271000	Flanking Active TSS	NH-A	brain
19	chr6:26269600-26271400	Weak transcription	Gastric	stomach
20	chr6:26269800-26272400	Active TSS	HMEC	breast
21	chr6:26269800-26274400	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr6:26269800-26274400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:26269800-26274800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:26269800-26274800	Active TSS	NHLF	lung
25	chr6:26270000-26271200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr6:26270000-26271200	Active TSS	Brain Germinal Matrix	brain
27	chr6:26270000-26271200	Flanking Active TSS	Fetal Stomach	stomach
28	chr6:26270000-26271400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr6:26270000-26271400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:26270000-26271400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:26270000-26272800	Flanking Active TSS	Fetal Thymus	thymus
32	chr6:26270000-26273000	Flanking Active TSS	NHEK	skin
33	chr6:26270000-26274200	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr6:26270000-26274600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:26270000-26274800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:26270200-26271200	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr6:26270200-26271600	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr6:26270200-26272000	Active TSS	Fetal Brain Female	brain
39	chr6:26270200-26272000	Active TSS	Fetal Kidney	kidney
40	chr6:26270200-26272800	Flanking Active TSS	HUVEC	blood vessel
41	chr6:26270200-26274400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:26270200-26274800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:26270400-26270800	Flanking Active TSS	Fetal Lung	lung
44	chr6:26270400-26270800	Flanking Active TSS	GM12878-XiMat	blood
45	chr6:26270400-26271000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:26270400-26271000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr6:26270400-26271000	Enhancers	Primary B cells from cord blood	blood
48	chr6:26270400-26271000	Enhancers	Primary T cells from cord blood	blood
49	chr6:26270400-26271200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:26270400-26271200	Enhancers	Primary B cells from peripheral blood	blood

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