Variant report

Variant	rs17279355
Chromosome Location	chr8:63922402-63922403
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	MYBL2	chr8:63922315-63922834	HepG2	liver:	n/a	n/a
2	EP300	chr8:63922313-63922850	HepG2	liver:	n/a	n/a
3	HNF4A	chr8:63922346-63922858	HepG2	liver:	n/a	chr8:63922573-63922585 chr8:63922552-63922567 chr8:63922571-63922586 chr8:63922572-63922586 chr8:63922571-63922586 chr8:63922572-63922585 chr8:63922572-63922580 chr8:63922572-63922584 chr8:63922573-63922585 chr8:63922571-63922586 chr8:63922571-63922586
4	POLR2A	chr8:63922340-63922860	HepG2	liver:	n/a	n/a
5	JUND	chr8:63922376-63922787	HepG2	liver:	n/a	chr8:63922686-63922696
6	HEY1	chr8:63922335-63922938	HepG2	liver:	n/a	n/a
7	POLR2A	chr8:63922399-63922576	HepG2	liver:	n/a	n/a
8	POLR2A	chr8:63922063-63922784	HepG2	liver:	n/a	n/a
9	POLR2A	chr8:63921001-63922934	HepG2	liver:	n/a	n/a
10	TBP	chr8:63921799-63922803	HepG2	liver:	n/a	n/a
11	HNF4A	chr8:63922305-63922802	HepG2	liver:	n/a	chr8:63922573-63922585 chr8:63922552-63922567 chr8:63922571-63922586 chr8:63922572-63922586 chr8:63922571-63922586 chr8:63922572-63922585 chr8:63922572-63922580 chr8:63922572-63922584 chr8:63922573-63922585 chr8:63922571-63922586 chr8:63922571-63922586
12	HEY1	chr8:63922212-63922856	HepG2	liver:	n/a	n/a
13	ARID3A	chr8:63922381-63923118	HepG2	liver:	n/a	n/a
14	RCOR1	chr8:63922261-63922813	HepG2	liver:	n/a	n/a
15	TEAD4	chr8:63922297-63922862	HepG2	liver:	n/a	n/a
16	SP1	chr8:63922333-63922863	HepG2	liver:	n/a	chr8:63922595-63922604
17	HNF4G	chr8:63922280-63922848	HepG2	liver:	n/a	chr8:63922573-63922585 chr8:63922571-63922586 chr8:63922572-63922586 chr8:63922571-63922586 chr8:63922553-63922568 chr8:63922572-63922587 chr8:63922572-63922585 chr8:63922572-63922580 chr8:63922572-63922584 chr8:63922573-63922585 chr8:63922571-63922586
18	HNF4G	chr8:63922319-63922803	HepG2	liver:	n/a	chr8:63922573-63922585 chr8:63922571-63922586 chr8:63922572-63922586 chr8:63922571-63922586 chr8:63922553-63922568 chr8:63922572-63922587 chr8:63922572-63922585 chr8:63922572-63922580 chr8:63922572-63922584 chr8:63922573-63922585 chr8:63922571-63922586

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:63896894..63899189-chr8:63921841..63923926,2	MCF-7	breast:
2	chr8:63917789..63919405-chr8:63920362..63922527,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240915	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10504360	0.93[ASN][1000 genomes]
rs10504361	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11545078	0.96[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.80[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11985884	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11985904	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11989852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11990678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11992253	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11993022	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16929879	0.82[ASN][1000 genomes]
rs16930045	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16930060	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16930066	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16930072	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17192653	0.93[ASN][1000 genomes]
rs17194931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902232	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1902233	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1902234	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1902235	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2124294	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2353363	0.98[ASN][1000 genomes]
rs2353364	0.98[ASN][1000 genomes]
rs28387373	0.82[ASN][1000 genomes]
rs2883148	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780129	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4395892	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4410897	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4419801	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55800505	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56034470	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56213868	0.98[ASN][1000 genomes]
rs56339102	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57069084	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57140769	0.82[AFR][1000 genomes]
rs57776226	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58942648	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59169978	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60751452	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60889737	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60897253	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61326296	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61518338	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61629446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508064	0.82[ASN][1000 genomes]
rs62508088	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508107	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62508108	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62508109	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62508110	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62508111	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508113	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508123	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508154	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508155	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508156	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508157	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508158	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6472063	0.95[ASN][1000 genomes]
rs66790008	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6983219	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6983643	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6983864	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6983896	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6997520	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7004087	0.90[JPT][hapmap]
rs7015120	0.81[ASN][1000 genomes]
rs7015302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72656550	0.93[ASN][1000 genomes]
rs72658344	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72658396	0.98[ASN][1000 genomes]
rs72658400	0.98[ASN][1000 genomes]
rs72659813	0.95[ASN][1000 genomes]
rs7834301	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018879	chr8:63281724-63937632	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1033527	chr8:63673915-64073735	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv6227	chr8:63892087-63936952	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17279355	GGH	cis	Nerve Tibial	GTEx
rs17279355	GGH	cis	Artery Tibial	GTEx
rs17279355	GGH	cis	Skin Sun Exposed Lower leg	GTEx
rs17279355	GGH	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:63906800-63926200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr8:63919200-63922800	Enhancers	Placenta	Placenta
3	chr8:63919400-63922600	Weak transcription	Thymus	Thymus
4	chr8:63919600-63924800	Enhancers	Primary B cells from peripheral blood	blood
5	chr8:63919800-63922600	Enhancers	Fetal Intestine Large	intestine
6	chr8:63919800-63922800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr8:63919800-63922800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr8:63919800-63922800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr8:63919800-63922800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr8:63919800-63922800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr8:63919800-63922800	Enhancers	Esophagus	oesophagus
12	chr8:63919800-63922800	Enhancers	Fetal Muscle Leg	muscle
13	chr8:63919800-63923000	Enhancers	Primary T cells from cord blood	blood
14	chr8:63919800-63923000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr8:63919800-63923600	Enhancers	Primary hematopoietic stem cells	blood
16	chr8:63919800-63924800	Enhancers	Fetal Intestine Small	intestine
17	chr8:63920000-63922800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr8:63920000-63922800	Enhancers	Fetal Thymus	thymus
19	chr8:63920000-63922800	Enhancers	HMEC	breast
20	chr8:63920200-63922800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
21	chr8:63920600-63923000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr8:63920600-63923200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr8:63920800-63922800	Enhancers	Small Intestine	intestine
24	chr8:63920800-63923000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
25	chr8:63920800-63935600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr8:63921000-63922800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr8:63921000-63923000	Flanking Active TSS	HepG2	liver
28	chr8:63921000-63923200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr8:63921000-63923400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
30	chr8:63921200-63923400	Enhancers	Brain Germinal Matrix	brain
31	chr8:63921200-63923800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr8:63921400-63922800	Enhancers	HSMMtube	muscle
33	chr8:63921600-63923600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr8:63921800-63922600	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr8:63921800-63922600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr8:63921800-63922800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr8:63922000-63922600	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr8:63922000-63922600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr8:63922000-63922600	Enhancers	HSMM	muscle
40	chr8:63922000-63922800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr8:63922000-63923000	Flanking Active TSS	GM12878-XiMat	blood
42	chr8:63922000-63923600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
43	chr8:63922000-63932000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr8:63922200-63922600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
45	chr8:63922200-63922600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr8:63922200-63922800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
47	chr8:63922200-63922800	Enhancers	Primary T cells fromperipheralblood	blood
48	chr8:63922200-63923600	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr8:63922200-63935600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr8:63922400-63922600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell

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