Variant report

Variant	rs6962710
Chromosome Location	chr7:140147902-140147903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:140137931..140140482-chr7:140145196..140147910,2	MCF-7	breast:
2	chr7:140147282..140150132-chr7:140156885..140159416,3	K562	blood:
3	chr7:139875694..139878627-chr7:140145539..140147917,2	K562	blood:
4	chr7:140147176..140149855-chr7:140152753..140155201,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260231	Chromatin interaction
ENSG00000006459	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10216203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs10224992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10226064	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10229678	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10231547	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10243155	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10244642	0.87[EUR][1000 genomes]
rs10256899	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10257079	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10258350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10267810	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10269611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10270875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10272040	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10272047	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10273061	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10275127	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10275142	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10278060	0.85[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10279172	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10280145	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10952680	0.91[EUR][1000 genomes]
rs11760895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11765962	0.87[EUR][1000 genomes]
rs11766079	0.96[EUR][1000 genomes]
rs11974068	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11978135	0.85[CEU][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12216619	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13438384	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13438583	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17161542	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17161569	1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs1969394	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2001941	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs2272096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2363824	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2363826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2363828	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28412759	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28439514	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28538447	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28553284	0.87[EUR][1000 genomes]
rs28563126	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28667371	0.87[EUR][1000 genomes]
rs28699169	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28784908	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28785875	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28832645	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2885922	0.85[CEU][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs28880113	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35747234	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4385389	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4424177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4427086	0.95[EUR][1000 genomes]
rs4431522	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55714045	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55833852	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55961611	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56059991	0.96[EUR][1000 genomes]
rs56769703	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58076938	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58647694	0.96[EUR][1000 genomes]
rs59814044	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60137728	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61577108	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62490410	0.87[EUR][1000 genomes]
rs62490429	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62490449	0.96[EUR][1000 genomes]
rs6464773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6464779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6951446	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6962593	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6963738	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6964170	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6966049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6966056	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6966930	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6968931	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6973069	0.85[EUR][1000 genomes]
rs6975307	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7777404	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7779827	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7784558	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7785094	0.92[GIH][hapmap]
rs7786776	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7787217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7789557	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7790232	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7800959	0.87[EUR][1000 genomes]
rs7805365	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7808589	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7811669	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9648837	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9692138	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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	nsv464734	chr7:140108096-140217670	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv608500	chr7:140108096-140217670	Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1803443	chr7:140146694-140263109	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6962710	JHDM1D	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140126400-140176600	Weak transcription	Right Atrium	heart
2	chr7:140126600-140148000	Weak transcription	Primary T cells from cord blood	blood
3	chr7:140133200-140154200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:140135800-140148600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr7:140135800-140151000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr7:140135800-140151000	Weak transcription	Fetal Brain Female	brain
7	chr7:140135800-140156000	Weak transcription	NHEK	skin
8	chr7:140136200-140149200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:140136600-140154600	Weak transcription	Fetal Brain Male	brain
10	chr7:140139200-140151400	Weak transcription	Fetal Intestine Large	intestine
11	chr7:140139400-140151200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:140139400-140152400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr7:140139600-140149000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr7:140139800-140149800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:140140600-140151600	Weak transcription	Fetal Intestine Small	intestine
16	chr7:140140800-140148600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:140140800-140153800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:140142000-140151600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:140142000-140154200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:140143600-140148800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr7:140144000-140149400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr7:140144000-140149400	Weak transcription	Lung	lung
23	chr7:140144000-140152600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:140144000-140152800	Weak transcription	Ovary	ovary
25	chr7:140144000-140153200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr7:140144000-140153800	Weak transcription	HepG2	liver
27	chr7:140144000-140154200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr7:140144000-140154200	Weak transcription	A549	lung
29	chr7:140144000-140154400	Weak transcription	Pancreas	Pancrea
30	chr7:140144200-140149400	Weak transcription	Fetal Stomach	stomach
31	chr7:140144200-140152600	Weak transcription	K562	blood
32	chr7:140144800-140153600	Weak transcription	Brain Germinal Matrix	brain
33	chr7:140145200-140152000	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr7:140145200-140152600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr7:140145800-140152800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr7:140146000-140153800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr7:140146400-140154400	Weak transcription	HMEC	breast
38	chr7:140146600-140153400	Weak transcription	Gastric	stomach
39	chr7:140146800-140153400	Weak transcription	Brain Hippocampus Middle	brain
40	chr7:140146800-140154400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr7:140147200-140148200	Enhancers	Primary B cells from peripheral blood	blood
42	chr7:140147200-140148400	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr7:140147200-140149000	Weak transcription	HSMMtube	muscle
44	chr7:140147200-140149800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr7:140147200-140150400	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr7:140147200-140153000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr7:140147400-140148000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr7:140147400-140148200	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr7:140147400-140149600	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr7:140147400-140149800	Enhancers	HUES48 Cell Line	embryonic stem cell

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