Variant report

Variant	rs957680
Chromosome Location	chr5:74055209-74055210
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:74054567..74056927-chr5:74071615..74073229,2	MCF-7	breast:
2	chr5:73980260..73982470-chr5:74054627..74056426,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000049860	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1048167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10515192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515199	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739122	0.84[LWK][hapmap];0.84[MKK][hapmap];0.81[YRI][hapmap]
rs11749137	0.81[YRI][hapmap]
rs11959570	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1350097	0.81[YRI][hapmap]
rs16872220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872259	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17561738	0.86[ASN][1000 genomes]
rs2061162	0.80[YRI][hapmap]
rs3733794	0.84[LWK][hapmap];0.84[MKK][hapmap];0.81[YRI][hapmap]
rs55899032	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55920995	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56127814	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56192858	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56203772	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57202395	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57549677	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58864890	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60492282	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6453076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453082	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6861935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6870806	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877442	0.81[YRI][hapmap]
rs6881400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6882035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882499	0.81[YRI][hapmap]
rs6883061	0.84[LWK][hapmap];0.84[MKK][hapmap];0.81[YRI][hapmap]
rs6883278	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6884338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884843	0.86[LWK][hapmap];0.87[MKK][hapmap]
rs6894177	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764630	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764643	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764647	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764648	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764650	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764654	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764655	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764656	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764657	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764663	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764669	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764675	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764676	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764683	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764684	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764687	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764690	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72766504	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7705519	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7713812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728889	0.81[YRI][hapmap]
rs7732440	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686657	0.86[LWK][hapmap];0.90[MKK][hapmap];0.81[YRI][hapmap]
rs9765469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598653	chr5:73992881-74095542	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs957680	GFM2	cis	parietal	SCAN
rs957680	TINP1	cis	normal skin	skin_eQTL
rs957680	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs957680	TINP1	cis	uninvolved skin	skin_eQTL
rs957680	TINP1	cis	multi-tissue	Pritchard
rs957680	TINP1	Cis_1M	lymphoblastoid	RTeQTL
rs957680	WDR41	cis	parietal	SCAN
rs957680	ZBED3	cis	parietal	SCAN
rs957680	NSA2	cis	Heart Left Ventricle	GTEx
rs957680	NSA2	cis	Whole Blood	GTEx
rs957680	NSA2	cis	Thyroid	GTEx
rs957680	NSA2	cis	cerebellum	SCAN
rs957680	NSA2	cis	Esophagus Mucosa	GTEx
rs957680	FAM169A	cis	Muscle Skeletal	GTEx
rs957680	NSA2	cis	Muscle Skeletal	GTEx
rs957680	NSA2	cis	parietal	SCAN
rs957680	NSA2	cis	Adipose Subcutaneous	GTEx
rs957680	NSA2	cis	Artery Aorta	GTEx
rs957680	NSA2	cis	Artery Tibial	GTEx
rs957680	NSA2	cis	Esophagus Muscularis	GTEx
rs957680	NSA2	cis	Nerve Tibial	GTEx
rs957680	NSA2	cis	Stomach	GTEx
rs957680	NSA2	cis	lymphoblastoid	seeQTL
rs957680	NSA2	cis	lung	GTEx
rs957680	TINP1	cis	lesional skin	skin_eQTL
rs957680	GFM2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73982000-74061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:73999800-74060800	Weak transcription	Pancreas	Pancrea
3	chr5:73999800-74062200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:74002600-74061800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:74008400-74060200	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr5:74008400-74060200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr5:74010400-74059600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:74018000-74060800	Weak transcription	Gastric	stomach
9	chr5:74018600-74062000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:74019200-74058600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:74021600-74060800	Weak transcription	Spleen	Spleen
12	chr5:74022000-74060800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:74025000-74062000	Weak transcription	Aorta	Aorta
14	chr5:74044400-74061000	Weak transcription	Fetal Heart	heart
15	chr5:74044400-74061000	Weak transcription	Right Ventricle	heart
16	chr5:74045000-74059600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:74045200-74061800	Weak transcription	Esophagus	oesophagus
18	chr5:74045800-74058800	Strong transcription	Primary T cells from cord blood	blood
19	chr5:74047400-74061800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:74048600-74055600	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr5:74049000-74056200	Weak transcription	Stomach Mucosa	stomach
22	chr5:74050000-74056600	Strong transcription	HSMM	muscle
23	chr5:74050400-74058000	Strong transcription	Fetal Intestine Large	intestine
24	chr5:74050800-74055400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:74050800-74059200	Strong transcription	Fetal Thymus	thymus
26	chr5:74051000-74056400	Strong transcription	HMEC	breast
27	chr5:74051000-74056800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:74051000-74059600	Strong transcription	Primary B cells from cord blood	blood
29	chr5:74051200-74060000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr5:74051400-74055400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr5:74051400-74058400	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:74051400-74059800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr5:74051400-74060200	Strong transcription	Liver	Liver
34	chr5:74051400-74061200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:74051600-74059600	Strong transcription	Placenta	Placenta
36	chr5:74051600-74059600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr5:74051600-74060000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:74051800-74058800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:74052000-74055800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:74052000-74056000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr5:74052000-74058800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr5:74052000-74059000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr5:74052000-74059200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr5:74052000-74059600	Strong transcription	Dnd41	blood
45	chr5:74052200-74056200	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr5:74052200-74056600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr5:74052200-74057200	Strong transcription	NH-A	brain
48	chr5:74052200-74059400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:74052200-74059400	Strong transcription	Adipose Nuclei	Adipose
50	chr5:74052200-74060400	Strong transcription	HUES48 Cell Line	embryonic stem cell

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