Variant report

Variant	rs1616534
Chromosome Location	chr8:11666451-11666452
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	STAT3	chr8:11666445-11666682	MCF10A-Er-Src	breast:	n/a	chr8:11666618-11666630
2	FOS	chr8:11666323-11666687	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr8:11666294-11666465	K562	blood:	n/a	n/a
4	SIN3AK20	chr8:11666314-11666713	PFSK-1	brain:	n/a	n/a
5	FOXA1	chr8:11666313-11666806	HepG2	liver:	n/a	chr8:11666537-11666552
6	POLR2A	chr8:11664775-11666889	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr8:11665396-11666911	PBDE	blood:	n/a	n/a
8	POLR2A	chr8:11664843-11666654	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr8:11666282-11666887	HepG2	liver:	n/a	n/a
10	TBL1XR1	chr8:11666352-11666589	K562	blood:	n/a	n/a
11	FOXA2	chr8:11666326-11666804	A549	lung:	n/a	n/a
12	FOXA1	chr8:11666223-11666802	HepG2	liver:	n/a	chr8:11666537-11666552
13	FOXA1	chr8:11666380-11666745	T-47D	breast:	n/a	chr8:11666537-11666552
14	FOXA2	chr8:11666174-11666781	A549	lung:	n/a	n/a
15	ARID3A	chr8:11666175-11666691	HepG2	liver:	n/a	n/a
16	POLR2A	chr8:11666401-11666593	MCF-7	breast:	n/a	n/a
17	MAX	chr8:11665583-11666571	A549	lung:	n/a	n/a
18	POLR2A	chr8:11665379-11666492	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr8:11665101-11666490	HepG2	liver:	n/a	n/a
20	HEY1	chr8:11664935-11666824	HepG2	liver:	n/a	chr8:11665851-11665866
21	MXI1	chr8:11665346-11666710	HepG2	liver:	n/a	n/a
22	TAL1	chr8:11666445-11666461	K562	blood:	n/a	n/a
23	POLR2A	chr8:11665410-11666524	HepG2	liver:	n/a	n/a
24	HDAC2	chr8:11666350-11666734	HepG2	liver:	n/a	chr8:11666542-11666551
25	GATA3	chr8:11666429-11666751	T-47D	breast:	n/a	n/a
26	EP300	chr8:11666235-11666468	HepG2	liver:	n/a	n/a
27	MYBL2	chr8:11666227-11666753	HepG2	liver:	n/a	n/a
28	POLR2A	chr8:11665392-11666606	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr8:11666110-11666702	HL-60	blood:	n/a	n/a
30	MAZ	chr8:11665275-11666823	IMR90	lung:	n/a	chr8:11666615-11666625
31	POLR2A	chr8:11665581-11666609	HL-60	blood:	n/a	n/a
32	CTCF	chr8:11666320-11666470	HAc	cerebellar:	n/a	n/a
33	POLR2A	chr8:11666282-11666586	HepG2	liver:	n/a	n/a
34	POLR2A	chr8:11665240-11666635	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr8:11666412-11666802	K562	blood:	n/a	n/a
36	POLR2A	chr8:11659475-11672720	K562	blood:	n/a	n/a
37	FOXA1	chr8:11666245-11666850	HepG2	liver:	n/a	chr8:11666537-11666552
38	HDAC2	chr8:11666198-11666509	K562	blood:	n/a	n/a
39	SIN3AK20	chr8:11666154-11666946	MCF-7	breast:	n/a	n/a
40	MXI1	chr8:11664826-11667052	SK-N-SH	brain:	n/a	n/a
41	HNF4A	chr8:11666438-11666763	HepG2	liver:	n/a	n/a
42	SMC3	chr8:11666389-11666722	HepG2	liver:	n/a	n/a
43	MYC	chr8:11666319-11666772	MCF10A-Er-Src	breast:	n/a	chr8:11666615-11666625
44	POLR2A	chr8:11666210-11666704	HepG2	liver:	n/a	n/a
45	KAP1	chr8:11666154-11666846	HEK293	kidney:	n/a	n/a
46	SIN3A	chr8:11665320-11666645	H1-hESC	embryonic stem cell:	n/a	chr8:11666073-11666087
47	TEAD4	chr8:11666034-11666560	K562	blood:	n/a	n/a
48	NFIC	chr8:11666333-11666713	HepG2	liver:	n/a	n/a
49	CTCF	chr8:11666380-11666530	BJ	skin:	n/a	n/a
50	ZNF263	chr8:11664943-11666666	HEK293-T-REx	kidney:	n/a	chr8:11665843-11665852

No.	Distal block	Cell Line	Cell type
1	chr8:11658127..11661675-chr8:11664375..11667732,3	K562	blood:
2	chr8:11665243..11667469-chr8:11710761..11712863,3	MCF-7	breast:
3	chr8:11625432..11628777-chr8:11664764..11667821,4	MCF-7	breast:
4	chr8:11663695..11667740-chr8:11686501..11689379,3	MCF-7	breast:
5	chr8:11658229..11662389-chr8:11662980..11669380,10	MCF-7	breast:
6	chr8:11664303..11666890-chr8:11705423..11707941,2	MCF-7	breast:

Variant related genes	Relation type
FDFT1	TF binding region
ENSG00000255046	Chromatin interaction
ENSG00000164733	Chromatin interaction
ENSG00000154328	Chromatin interaction
ENSG00000079459	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1032575	0.91[EUR][1000 genomes]
rs1032577	0.88[EUR][1000 genomes]
rs13258488	0.82[CEU][hapmap]
rs1497042	0.81[AMR][1000 genomes]
rs1618110	0.87[ASN][1000 genomes]
rs1619667	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1736057	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1736060	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1736067	0.82[CHD][hapmap]
rs1736070	0.83[ASN][1000 genomes]
rs2179010	0.92[EUR][1000 genomes]
rs2252567	0.81[AMR][1000 genomes]
rs2409836	0.81[TSI][hapmap]
rs4841600	0.81[TSI][hapmap]
rs7001819	0.92[CEU][hapmap]
rs904015	0.82[CEU][hapmap]

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	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
18	nsv890365	chr8:11666451-11735641	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv890366	chr8:11666451-11900847	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription 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	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1616534	FLJ10661	cis	cerebellum	SCAN
rs1616534	PPP1R3B	cis	cerebellum	SCAN
rs1616534	MFHAS1	cis	cerebellum	SCAN
rs1616534	C8orf48	cis	cerebellum	SCAN
rs1616534	FDFT1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11658400-11666800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr8:11660400-11668200	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr8:11661000-11667200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:11662400-11666800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
5	chr8:11662400-11666800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr8:11662600-11667000	Transcr. at gene 5' and 3'	NHEK	skin
7	chr8:11664200-11669000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr8:11664600-11666600	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr8:11664800-11666800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr8:11664800-11667000	Weak transcription	Hela-S3	cervix
11	chr8:11665000-11667000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr8:11665000-11667200	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr8:11665200-11666600	Active TSS	NHDF-Ad	bronchial
14	chr8:11665200-11666800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr8:11665200-11667000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr8:11665200-11667200	Active TSS	Ovary	ovary
17	chr8:11665400-11666600	Active TSS	Lung	lung
18	chr8:11665400-11666600	Active TSS	A549	lung
19	chr8:11665400-11666800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr8:11665400-11666800	Active TSS	Psoas Muscle	Psoas
21	chr8:11665400-11667000	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr8:11665400-11667000	Active TSS	Fetal Brain Female	brain
23	chr8:11665400-11667200	Active TSS	Brain Anterior Caudate	brain
24	chr8:11665400-11667200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr8:11665600-11666600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr8:11665600-11666600	Active TSS	Brain Hippocampus Middle	brain
27	chr8:11665600-11666600	Active TSS	Esophagus	oesophagus
28	chr8:11665600-11666600	Active TSS	Fetal Kidney	kidney
29	chr8:11665600-11666600	Active TSS	Gastric	stomach
30	chr8:11665600-11666600	Active TSS	Pancreas	Pancrea
31	chr8:11665600-11666600	Active TSS	Stomach Mucosa	stomach
32	chr8:11665600-11666600	Active TSS	GM12878-XiMat	blood
33	chr8:11665600-11666800	Active TSS	Fetal Intestine Large	intestine
34	chr8:11665600-11666800	Active TSS	Fetal Stomach	stomach
35	chr8:11665600-11666800	Active TSS	HSMMtube	muscle
36	chr8:11665600-11667000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr8:11665600-11667000	Active TSS	Aorta	Aorta
38	chr8:11665600-11667200	Active TSS	Brain Cingulate Gyrus	brain
39	chr8:11665600-11667200	Active TSS	Brain Substantia Nigra	brain
40	chr8:11665600-11667200	Active TSS	Colon Smooth Muscle	Colon
41	chr8:11665600-11667200	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr8:11665600-11667200	Active TSS	Left Ventricle	heart
43	chr8:11665600-11667200	Active TSS	Right Ventricle	heart
44	chr8:11665800-11666600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr8:11665800-11666600	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr8:11665800-11666600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr8:11665800-11666600	Active TSS	Fetal Lung	lung
48	chr8:11665800-11666600	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr8:11665800-11666600	Active TSS	NHLF	lung
50	chr8:11665800-11666600	Active TSS	Osteobl	bone

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