Variant report

Variant	rs6901686
Chromosome Location	chr6:29715721-29715722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr6:29715680-29715880	HepG2	liver:	n/a	n/a
2	SIN3A	chr6:29715713-29717573	H1-hESC	embryonic stem cell:	n/a	chr6:29717251-29717262 chr6:29717074-29717085
3	POLR2A	chr6:29715691-29717474	K562	blood:	n/a	n/a
4	MAZ	chr6:29715717-29715725	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29713370..29715869-chr6:29729277..29731286,2	MCF-7	breast:

Variant related genes	Relation type
HCG9P5	TF binding region
ENSG00000199290	TF binding region
ENSG00000270896	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1633066	0.87[ASN][1000 genomes]
rs1736913	0.83[ASN][1000 genomes]
rs1736919	0.82[ASN][1000 genomes]
rs1737069	0.86[ASN][1000 genomes]
rs2072894	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072896	0.92[ASN][1000 genomes]
rs2075682	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2076174	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272874	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3734813	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3734815	0.89[ASN][1000 genomes]
rs3736694	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3736697	0.92[ASN][1000 genomes]
rs3757324	0.91[ASN][1000 genomes]
rs3757325	0.91[ASN][1000 genomes]
rs3757326	0.91[ASN][1000 genomes]
rs3817826	0.85[ASN][1000 genomes]
rs3823318	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6910733	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7739360	0.83[ASN][1000 genomes]
rs7739388	0.83[ASN][1000 genomes]
rs7741597	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7742523	0.92[ASN][1000 genomes]
rs7751815	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7753946	0.95[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7754692	0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7755571	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7759272	0.83[ASN][1000 genomes]
rs7773358	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9258156	0.83[ASN][1000 genomes]
rs9258158	0.90[ASN][1000 genomes]
rs9258160	0.90[ASN][1000 genomes]
rs9258163	0.91[ASN][1000 genomes]
rs9258164	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9258166	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9258167	0.91[ASN][1000 genomes]
rs9258168	0.91[ASN][1000 genomes]
rs9258169	0.91[ASN][1000 genomes]
rs9258170	0.91[ASN][1000 genomes]
rs9258171	0.91[ASN][1000 genomes]
rs9258172	0.91[ASN][1000 genomes]
rs9258173	0.91[ASN][1000 genomes]
rs9258174	0.91[ASN][1000 genomes]
rs9258175	0.91[ASN][1000 genomes]
rs9258176	0.80[ASN][1000 genomes]
rs9258187	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9258192	0.92[ASN][1000 genomes]
rs9258203	0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9258205	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9258207	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9258211	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9258212	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9258214	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9258215	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9258216	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9258218	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9258222	0.89[AFR][1000 genomes]
rs9258223	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9258224	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258225	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258226	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9258227	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9258228	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9258229	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9258230	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258236	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9258242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258244	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258258	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258259	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258260	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258262	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258265	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9258272	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9258274	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv883533	chr6:29704237-29715997	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv883534	chr6:29708222-29724310	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6901686	HLA-F	cis	multi-tissue	Pritchard

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29692200-29715800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:29692400-29715800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:29693800-29716000	Weak transcription	Small Intestine	intestine
4	chr6:29696800-29715800	Weak transcription	Colonic Mucosa	Colon
5	chr6:29706000-29715800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:29706800-29715800	Weak transcription	NHDF-Ad	bronchial
7	chr6:29712800-29716000	Weak transcription	Aorta	Aorta
8	chr6:29714600-29715800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr6:29714800-29715800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr6:29714800-29715800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:29715000-29715800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr6:29715000-29715800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:29715200-29715800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
14	chr6:29715200-29715800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr6:29715200-29715800	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr6:29715200-29715800	Flanking Active TSS	HMEC	breast
17	chr6:29715200-29717200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:29715400-29715800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:29715400-29715800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr6:29715400-29715800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:29715400-29715800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:29715400-29715800	Enhancers	Gastric	stomach
23	chr6:29715400-29715800	Enhancers	Left Ventricle	heart
24	chr6:29715400-29715800	Enhancers	Lung	lung
25	chr6:29715400-29715800	Enhancers	Pancreas	Pancrea
26	chr6:29715400-29715800	Enhancers	Right Atrium	heart
27	chr6:29715400-29715800	Enhancers	Spleen	Spleen
28	chr6:29715400-29715800	Enhancers	GM12878-XiMat	blood
29	chr6:29715400-29715800	Enhancers	K562	blood
30	chr6:29715400-29716000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:29715400-29716000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:29715400-29716000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
33	chr6:29715400-29716000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
34	chr6:29715400-29716000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:29715400-29716000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr6:29715400-29716200	Flanking Active TSS	Hela-S3	cervix
37	chr6:29715400-29717400	Active TSS	H9 Cell Line	embryonic stem cell
38	chr6:29715400-29717600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr6:29715400-29717800	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr6:29715600-29715800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:29715600-29715800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:29715600-29715800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:29715600-29715800	Enhancers	Muscle Satellite Cultured Cells	--
44	chr6:29715600-29715800	Enhancers	Adipose Nuclei	Adipose
45	chr6:29715600-29715800	Enhancers	Brain Anterior Caudate	brain
46	chr6:29715600-29715800	Enhancers	Brain Cingulate Gyrus	brain
47	chr6:29715600-29715800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
48	chr6:29715600-29715800	Active TSS	Ovary	ovary
49	chr6:29715600-29715800	Enhancers	Placenta Amnion	Placenta Amnion
50	chr6:29715600-29715800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum

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