Variant report

Variant	rs17279320
Chromosome Location	chr8:63921513-63921514
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	POLR2A	chr8:63921186-63922200	HepG2	liver:	n/a	n/a
2	POLR2A	chr8:63921001-63922934	HepG2	liver:	n/a	n/a
3	POLR2A	chr8:63921203-63921572	H1-neurons	neurons:	n/a	n/a
4	TEAD4	chr8:63920976-63921533	HepG2	liver:	n/a	n/a

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

Variant related genes	Relation type
ENSG00000240915	TF binding region

Extended variants
information (count: 84 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10504360	0.93[ASN][1000 genomes]
rs10504361	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11545078	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11985884	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11985904	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11989852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11990678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11992253	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11993022	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16929879	0.82[ASN][1000 genomes]
rs16930045	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16930060	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16930066	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16930072	0.83[AMR][1000 genomes];0.98[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279355	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[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902232	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1902233	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1902234	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1902235	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2124294	0.94[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	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780129	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4395892	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4410897	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4419801	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55800505	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56034470	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56213868	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56339102	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57069084	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57776226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58942648	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59169978	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60751452	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60889737	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60897253	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61326296	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61518338	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61629446	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508064	0.82[ASN][1000 genomes]
rs62508088	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508107	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62508108	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62508109	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62508110	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62508111	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508113	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508123	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508154	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508155	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508156	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508157	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508158	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510060	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510063	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6472063	0.95[ASN][1000 genomes]
rs66790008	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6983219	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6983643	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6983864	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6983896	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6997520	0.88[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];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72656550	0.93[ASN][1000 genomes]
rs72658344	1.00[AMR][1000 genomes];1.00[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17279320	GGH	cis	Artery Tibial	GTEx
rs17279320	GGH	cis	Adipose Subcutaneous	GTEx
rs17279320	GGH	Cis_1M	lymphoblastoid	RTeQTL
rs17279320	GGH	cis	Skin Sun Exposed Lower leg	GTEx
rs17279320	GGH	cis	Nerve Tibial	GTEx

Chromatin state (count:60 , 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	chr8:63915600-63922200	Weak transcription	Fetal Kidney	kidney
3	chr8:63919200-63922800	Enhancers	Placenta	Placenta
4	chr8:63919400-63922600	Weak transcription	Thymus	Thymus
5	chr8:63919600-63924800	Enhancers	Primary B cells from peripheral blood	blood
6	chr8:63919800-63921800	Enhancers	Primary T cells fromperipheralblood	blood
7	chr8:63919800-63921800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr8:63919800-63922400	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr8:63919800-63922400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr8:63919800-63922600	Enhancers	Fetal Intestine Large	intestine
11	chr8:63919800-63922800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:63919800-63922800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr8:63919800-63922800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr8:63919800-63922800	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr8:63919800-63922800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr8:63919800-63922800	Enhancers	Esophagus	oesophagus
17	chr8:63919800-63922800	Enhancers	Fetal Muscle Leg	muscle
18	chr8:63919800-63923000	Enhancers	Primary T cells from cord blood	blood
19	chr8:63919800-63923000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr8:63919800-63923600	Enhancers	Primary hematopoietic stem cells	blood
21	chr8:63919800-63924800	Enhancers	Fetal Intestine Small	intestine
22	chr8:63920000-63922000	Enhancers	GM12878-XiMat	blood
23	chr8:63920000-63922800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr8:63920000-63922800	Enhancers	Fetal Thymus	thymus
25	chr8:63920000-63922800	Enhancers	HMEC	breast
26	chr8:63920200-63922800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
27	chr8:63920400-63921800	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr8:63920400-63922200	Enhancers	Primary B cells from cord blood	blood
29	chr8:63920600-63921600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr8:63920600-63922000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr8:63920600-63922000	Enhancers	Duodenum Mucosa	Duodenum
32	chr8:63920600-63922000	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr8:63920600-63923000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr8:63920600-63923200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr8:63920800-63921800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr8:63920800-63922400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
37	chr8:63920800-63922400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr8:63920800-63922400	Enhancers	Colonic Mucosa	Colon
39	chr8:63920800-63922800	Enhancers	Small Intestine	intestine
40	chr8:63920800-63923000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
41	chr8:63920800-63935600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr8:63921000-63921800	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr8:63921000-63922000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr8:63921000-63922000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr8:63921000-63922400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
46	chr8:63921000-63922800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr8:63921000-63923000	Flanking Active TSS	HepG2	liver
48	chr8:63921000-63923200	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr8:63921000-63923400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
50	chr8:63921200-63921600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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