Variant report

Variant	rs12665501
Chromosome Location	chr6:31508069-31508070
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:31508060-31508210	GM12869	blood:	n/a	n/a
2	POLR2A	chr6:31505026-31508472	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:31507034-31508750	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:31507830-31508165	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:31507884-31508418	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr6:31507929-31508407	GM12892	blood:	n/a	n/a
7	POLR2A	chr6:31505312-31508500	GM12878	blood:	n/a	n/a
8	WRNIP1	chr6:31507662-31510318	GM12878	blood:	n/a	n/a
9	POLR2A	chr6:31507959-31508464	K562	blood:	n/a	n/a
10	POLR2A	chr6:31507858-31508411	GM12892	blood:	n/a	n/a
11	POLR2A	chr6:31507994-31508193	K562	blood:	n/a	n/a
12	POLR2A	chr6:31506089-31508478	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:31507994-31508082	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr6:31507881-31508341	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr6:31507664-31508425	K562	blood:	n/a	n/a
16	HEY1	chr6:31506024-31508418	K562	blood:	n/a	n/a
17	POLR2A	chr6:31506295-31508505	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr6:31508046-31508106	HepG2	liver:	n/a	n/a
19	POLR2A	chr6:31505819-31511508	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr6:31507923-31508472	GM12891	blood:	n/a	n/a
21	TAL1	chr6:31508011-31508082	K562	blood:	n/a	n/a
22	MXI1	chr6:31507514-31511487	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr6:31507792-31511234	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr6:31507608-31508526	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr6:31507733-31511078	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr6:31507867-31508101	Hela-S3	cervix:	n/a	n/a

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31507549..31510479-chr6:31669713..31671247,2	MCF-7	breast:
2	chr6:31507082..31511713-chr6:31583957..31591905,17	MCF-7	breast:
3	chr6:31506561..31512642-chr6:31697539..31702106,5	K562	blood:
4	chr6:31507867..31510784-chr6:31781026..31784406,3	MCF-7	breast:
5	chr6:31507451..31516055-chr6:31617949..31624791,11	MCF-7	breast:
6	chr6:31506496..31512275-chr6:31630248..31634828,11	K562	blood:
7	chr6:31459710..31467567-chr6:31506191..31511027,18	MCF-7	breast:
8	chr6:31504619..31508588-chr6:31538806..31541615,4	K562	blood:
9	chr6:31506740..31512488-chr6:31586502..31592966,30	K562	blood:
10	chr6:31507082..31510843-chr6:31599707..31603450,4	K562	blood:
11	chr6:31506595..31512441-chr6:31585525..31590767,30	K562	blood:
12	chr6:31506529..31508833-chr6:31606767..31610616,4	K562	blood:
13	chr6:31507205..31511686-chr6:31618024..31622039,13	K562	blood:
14	chr6:31458384..31468965-chr6:31503613..31512721,28	K562	blood:
15	chr6:31506998..31509094-chr6:31864561..31866443,2	MCF-7	breast:
16	chr6:31507998..31511841-chr6:31541735..31545245,5	MCF-7	breast:
17	chr6:31507710..31510101-chr6:31604073..31606097,3	K562	blood:
18	chr6:31507406..31516955-chr6:31615847..31623354,26	K562	blood:
19	chr6:31507927..31511187-chr6:31633283..31638231,4	MCF-7	breast:
20	chr6:31505350..31512312-chr6:31630543..31635379,11	K562	blood:
21	chr6:31505549..31508168-chr6:31560722..31562471,2	K562	blood:
22	chr6:31506029..31511048-chr6:31626239..31630287,7	MCF-7	breast:
23	chr6:31507058..31511692-chr6:31586700..31590601,11	MCF-7	breast:
24	chr6:31460486..31468205-chr6:31503942..31512721,23	K562	blood:
25	chr6:31504619..31510971-chr6:31539361..31543067,6	K562	blood:
26	chr6:31507944..31511146-chr6:31743964..31746169,3	K562	blood:

No data

Variant related genes	Relation type
SNORD117	TF binding region
DDX39B-AS1	TF binding region
DDX39B	TF binding region
ENSG00000204516	Chromatin interaction
ENSG00000200816	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000201680	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000204389	Chromatin interaction
ENSG00000204371	Chromatin interaction
ENSG00000204469	Chromatin interaction
ENSG00000204475	Chromatin interaction
ENSG00000166278	Chromatin interaction
ENSG00000204394	Chromatin interaction
ENSG00000213722	Chromatin interaction
ENSG00000226979	Chromatin interaction
ENSG00000232810	Chromatin interaction
ENSG00000240053	Chromatin interaction
ENSG00000201207	Chromatin interaction
ENSG00000204439	Chromatin interaction
ENSG00000204390	Chromatin interaction
ENSG00000204396	Chromatin interaction
ENSG00000204444	Chromatin interaction
ENSG00000204463	Chromatin interaction
ENSG00000204427	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12662306	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665489	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71563350	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
2	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
3	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
4	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
5	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
6	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
7	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
8	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
9	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
10	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
11	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
12	nsv1018463	chr6:31337336-31525275	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
13	nsv538189	chr6:31337336-31525275	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
14	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
15	esv2757162	chr6:31353329-31542308	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
16	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
17	nsv432877	chr6:31412961-31528690	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
18	nsv830627	chr6:31496214-31659950	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
19	nsv470809	chr6:31496915-31544189	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31503800-31508200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
2	chr6:31504400-31508400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:31505400-31508400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
4	chr6:31505600-31508400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:31505600-31508800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:31506000-31508200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:31506000-31508400	Genic enhancers	Spleen	Spleen
8	chr6:31506000-31508600	Transcr. at gene 5' and 3'	Hela-S3	cervix
9	chr6:31506200-31508200	Genic enhancers	Small Intestine	intestine
10	chr6:31506200-31508400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
11	chr6:31506200-31508800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:31506200-31509400	Transcr. at gene 5' and 3'	Dnd41	blood
13	chr6:31506400-31508200	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:31506400-31508200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:31506400-31508200	Genic enhancers	Brain Substantia Nigra	brain
16	chr6:31506400-31508200	Transcr. at gene 5' and 3'	NH-A	brain
17	chr6:31506400-31508400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
18	chr6:31506400-31508400	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:31506400-31508400	Transcr. at gene 5' and 3'	HUVEC	blood vessel
20	chr6:31506400-31509000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
21	chr6:31506400-31509000	Transcr. at gene 5' and 3'	NHEK	skin
22	chr6:31506600-31508200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:31506600-31508200	Genic enhancers	Primary monocytes fromperipheralblood	blood
24	chr6:31506600-31508200	Genic enhancers	Brain Angular Gyrus	brain
25	chr6:31506600-31508200	Genic enhancers	Placenta	Placenta
26	chr6:31506600-31508200	Transcr. at gene 5' and 3'	HMEC	breast
27	chr6:31506600-31508200	Transcr. at gene 5' and 3'	NHLF	lung
28	chr6:31506600-31508400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:31506600-31508400	Genic enhancers	Placenta Amnion	Placenta Amnion
30	chr6:31506600-31508800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:31506600-31509000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
32	chr6:31506600-31510400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:31506800-31508200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:31506800-31508200	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
35	chr6:31506800-31508200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
36	chr6:31506800-31508400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
37	chr6:31506800-31508400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
38	chr6:31506800-31508400	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
39	chr6:31506800-31508400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:31506800-31508400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:31506800-31508400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
42	chr6:31506800-31508400	Transcr. at gene 5' and 3'	Fetal Lung	lung
43	chr6:31506800-31508400	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
44	chr6:31506800-31508400	Transcr. at gene 5' and 3'	HepG2	liver
45	chr6:31506800-31508400	Transcr. at gene 5' and 3'	Osteobl	bone
46	chr6:31506800-31508600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
47	chr6:31506800-31509000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
48	chr6:31506800-31509000	Transcr. at gene 5' and 3'	A549	lung
49	chr6:31506800-31509200	Transcr. at gene 5' and 3'	K562	blood
50	chr6:31506800-31509400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell

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