Variant report

Variant	rs12056541
Chromosome Location	chr8:11659703-11659704
allele	C/T
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	POLR2A	chr8:11659699-11660476	GM12891	blood:	n/a	n/a
2	HCFC1	chr8:11659437-11661136	Hela-S3	cervix:	n/a	n/a
3	TBP	chr8:11659420-11660837	HepG2	liver:	n/a	n/a
4	POLR2A	chr8:11659473-11661258	K562	blood:	n/a	n/a
5	TBP	chr8:11659371-11660473	H1-hESC	embryonic stem cell:	n/a	n/a
6	NFYB	chr8:11659506-11660607	GM12878	blood:	n/a	chr8:11660112-11660124 chr8:11660081-11660093 chr8:11660079-11660094 chr8:11660113-11660128 chr8:11660115-11660125 chr8:11660113-11660128 chr8:11660113-11660127 chr8:11660033-11660043
7	EP300	chr8:11659681-11660256	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr8:11659699-11660940	HepG2	liver:	n/a	n/a
9	POLR2A	chr8:11659657-11660778	Hela-S3	cervix:	n/a	n/a
10	MYC	chr8:11659671-11660350	MCF10A-Er-Src	breast:	n/a	chr8:11659821-11659832 chr8:11659824-11659833 chr8:11659821-11659831
11	POLR2A	chr8:11659602-11660928	MCF-7	breast:	n/a	n/a
12	REST	chr8:11659683-11660500	A549	lung:	n/a	chr8:11659737-11659750
13	SP1	chr8:11659526-11660508	H1-hESC	embryonic stem cell:	n/a	chr8:11660186-11660198 chr8:11660466-11660475 chr8:11660070-11660091 chr8:11660198-11660210 chr8:11660200-11660209 chr8:11660198-11660210 chr8:11660466-11660475 chr8:11660465-11660474 chr8:11660114-11660135 chr8:11660186-11660198
14	TAF1	chr8:11659562-11660488	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr8:11659382-11660850	GM12892	blood:	n/a	n/a
16	E2F6	chr8:11659455-11660498	H1-hESC	embryonic stem cell:	n/a	chr8:11660465-11660477 chr8:11660199-11660208 chr8:11660190-11660199 chr8:11660115-11660124 chr8:11660081-11660090
17	POLR2A	chr8:11659563-11660048	HepG2	liver:	n/a	n/a
18	MAZ	chr8:11659492-11661341	IMR90	lung:	n/a	chr8:11659821-11659832 chr8:11659824-11659833 chr8:11659821-11659831
19	POLR2A	chr8:11659352-11660997	GM18505	blood:	n/a	n/a
20	POLR2A	chr8:11659628-11660063	A549	lung:	n/a	n/a
21	FOXA2	chr8:11659468-11660070	HepG2	liver:	n/a	n/a
22	RELA	chr8:11659637-11661100	GM15510	blood:	n/a	n/a
23	CHD2	chr8:11659507-11660440	H1-hESC	embryonic stem cell:	n/a	n/a
24	TCF12	chr8:11659476-11660901	ECC-1	luminal epithelium:	n/a	chr8:11660455-11660465
25	POLR2A	chr8:11659417-11661294	GM18951	blood:	n/a	n/a
26	MAX	chr8:11659548-11661745	Hela-S3	cervix:	n/a	chr8:11659821-11659832 chr8:11661370-11661381 chr8:11659824-11659833 chr8:11659821-11659831
27	FOXA1	chr8:11659587-11660210	HepG2	liver:	n/a	n/a
28	POLR2A	chr8:11659331-11660693	HUVEC	blood vessel:	n/a	n/a
29	GATA1	chr8:11659383-11661536	K562	blood:	n/a	chr8:11660827-11660836 chr8:11661051-11661061 chr8:11661052-11661061
30	POLR2A	chr8:11659556-11660926	HUVEC	blood vessel:	n/a	n/a
31	SP4	chr8:11659509-11660566	H1-hESC	embryonic stem cell:	n/a	n/a
32	FOXA1	chr8:11659431-11660398	HepG2	liver:	n/a	n/a
33	STAT5A	chr8:11659468-11660090	GM12878	blood:	n/a	n/a
34	POLR2A	chr8:11659547-11660064	GM12891	blood:	n/a	n/a
35	NFIC	chr8:11659529-11660060	HepG2	liver:	n/a	n/a
36	SIN3AK20	chr8:11659680-11660091	A549	lung:	n/a	n/a
37	REST	chr8:11659597-11660574	H1-neurons	neurons:	n/a	chr8:11659737-11659750
38	CHD2	chr8:11659647-11660934	Hela-S3	cervix:	n/a	n/a
39	TEAD4	chr8:11659411-11661349	K562	blood:	n/a	chr8:11659549-11659558
40	CREB1	chr8:11659357-11660952	HepG2	liver:	n/a	n/a
41	TAF1	chr8:11659477-11660571	H1-neurons	neurons:	n/a	n/a
42	SMARCB1	chr8:11659647-11660937	Hela-S3	cervix:	n/a	n/a
43	SMC3	chr8:11659562-11660445	Hela-S3	cervix:	n/a	chr8:11660325-11660335
44	FOXA1	chr8:11659634-11660089	HepG2	liver:	n/a	n/a
45	USF1	chr8:11659654-11660537	ECC-1	luminal epithelium:	n/a	chr8:11660162-11660178 chr8:11660194-11660210
46	E2F6	chr8:11659374-11661028	K562	blood:	n/a	chr8:11660465-11660477 chr8:11660199-11660208 chr8:11660190-11660199 chr8:11660115-11660124 chr8:11660636-11660646 chr8:11660081-11660090
47	MAZ	chr8:11659642-11660894	GM12878	blood:	n/a	chr8:11659821-11659832 chr8:11659824-11659833 chr8:11659821-11659831
48	RCOR1	chr8:11659580-11661038	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr8:11659567-11660470	HepG2	liver:	n/a	n/a
50	FOXA2	chr8:11659476-11660328	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:11645433..11648215-chr8:11658187..11661640,5	MCF-7	breast:
2	chr11:2398309..2399006-chr8:11659548..11660515,2	HCT-116	colon:
3	chr8:11658330..11660255-chr8:11664033..11666074,2	MCF-7	breast:
4	chr8:11658864..11661745-chr8:11724576..11726431,3	MCF-7	breast:
5	chr8:11658229..11662389-chr8:11662980..11669380,10	MCF-7	breast:
6	chr8:11652587..11657894-chr8:11658127..11661459,7	K562	blood:
7	chr8:11659426..11661474-chr8:11724613..11726870,3	MCF-7	breast:
8	chr8:11625747..11629309-chr8:11658765..11661345,4	K562	blood:
9	chr8:11658127..11661675-chr8:11664375..11667732,3	K562	blood:
10	chr8:11626596..11628658-chr8:11659514..11662088,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-297N6.4.1-1	chr8:11659431-11660021	NONHSAT125085

Variant related genes	Relation type
FDFT1	TF binding region
ENSG00000227203	Chromatin interaction
ENSG00000110651	Chromatin interaction
ENSG00000154328	Chromatin interaction
ENSG00000079459	Chromatin interaction
ENSG00000164733	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11995135	0.80[EUR][1000 genomes]
rs2280922	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9650662	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1023803	chr8:11623570-11721655	Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv539476	chr8:11623570-11721655	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv890361	chr8:11625808-11755513	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv890362	chr8:11625808-11771089	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1032739	chr8:11643803-11716473	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv890363	chr8:11647941-11681825	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv890364	chr8:11654796-11671041	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv1034132	chr8:11657033-12198242	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 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	chr8:11657800-11659800	Flanking Active TSS	Dnd41	blood
2	chr8:11658400-11659800	Flanking Active TSS	HepG2	liver
3	chr8:11658400-11666800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr8:11658600-11659800	Flanking Active TSS	K562	blood
5	chr8:11659000-11659800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr8:11659000-11663400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr8:11659200-11659800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr8:11659200-11659800	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr8:11659200-11659800	Flanking Active TSS	GM12878-XiMat	blood
10	chr8:11659200-11661200	Active TSS	Brain Hippocampus Middle	brain
11	chr8:11659200-11663200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr8:11659400-11659800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr8:11659400-11659800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr8:11659400-11659800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr8:11659400-11659800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr8:11659400-11659800	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr8:11659400-11659800	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr8:11659400-11659800	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr8:11659400-11659800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr8:11659400-11659800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr8:11659400-11659800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr8:11659400-11659800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr8:11659400-11659800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr8:11659400-11659800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr8:11659400-11659800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr8:11659400-11659800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr8:11659400-11659800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr8:11659400-11659800	Flanking Active TSS	Liver	Liver
29	chr8:11659400-11659800	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr8:11659400-11659800	Flanking Active TSS	Brain Germinal Matrix	brain
31	chr8:11659400-11659800	Flanking Active TSS	Brain Substantia Nigra	brain
32	chr8:11659400-11659800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr8:11659400-11659800	Flanking Active TSS	Fetal Intestine Large	intestine
34	chr8:11659400-11659800	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr8:11659400-11659800	Flanking Active TSS	Fetal Muscle Leg	muscle
36	chr8:11659400-11659800	Flanking Active TSS	Placenta	Placenta
37	chr8:11659400-11659800	Flanking Active TSS	Fetal Stomach	stomach
38	chr8:11659400-11659800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr8:11659400-11659800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr8:11659400-11659800	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr8:11659400-11659800	Flanking Active TSS	Thymus	Thymus
42	chr8:11659400-11659800	Flanking Active TSS	HMEC	breast
43	chr8:11659400-11659800	Flanking Active TSS	HSMMtube	muscle
44	chr8:11659400-11659800	Flanking Active TSS	NHDF-Ad	bronchial
45	chr8:11659400-11659800	Flanking Active TSS	NHEK	skin
46	chr8:11659400-11659800	Flanking Active TSS	Osteobl	bone
47	chr8:11659400-11660000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr8:11659400-11660000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr8:11659400-11660000	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr8:11659400-11660000	Flanking Active TSS	Primary T cells fromperipheralblood	blood

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