Variant report

Variant	rs6962772
Chromosome Location	chr7:99081730-99081731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99070549..99074806-chr7:99079713..99086160,8	K562	blood:
2	chr7:99070395..99072664-chr7:99081646..99084913,3	MCF-7	breast:
3	chr7:99036051..99038082-chr7:99079952..99081854,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZKSCAN5-1	chr7:99081653-99081766	NONHSAT122247

Variant related genes	Relation type
ENSG00000160917	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000198556	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1011024	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10155966	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs10225314	0.87[JPT][hapmap]
rs10238965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10243678	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs10244158	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253937	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10254729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10258757	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap]
rs10270459	0.92[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs10270917	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap]
rs10271049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10271582	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10272998	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[MEX][hapmap]
rs10279308	0.84[CEU][hapmap]
rs1043466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10464604	0.82[ASN][1000 genomes]
rs11539770	0.82[ASN][1000 genomes]
rs11762273	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap]
rs11772470	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11976018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11978089	0.84[CEU][hapmap]
rs12538826	0.83[ASN][1000 genomes]
rs13227795	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13240600	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13437771	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2003499	0.84[CEU][hapmap]
rs2072181	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs2240384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240385	0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2272168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280600	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2280601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286162	0.92[CEU][hapmap]
rs2404324	0.93[EUR][1000 genomes]
rs28457808	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28495024	0.81[AMR][1000 genomes]
rs3137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34777615	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3779354	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3800960	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs3801288	0.92[CEU][hapmap];0.90[MEX][hapmap]
rs3843540	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3901286	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45492098	0.81[ASN][1000 genomes]
rs45540134	0.87[ASN][1000 genomes]
rs45622743	0.84[ASN][1000 genomes]
rs4646450	0.82[ASW][hapmap];0.85[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs4729532	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs58222677	0.84[ASN][1000 genomes]
rs61159815	0.86[ASN][1000 genomes]
rs61402640	0.81[ASN][1000 genomes]
rs61543997	0.81[ASN][1000 genomes]
rs6943920	0.91[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap]
rs6955490	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs6961634	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7794682	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7794705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7804551	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs868564	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs883403	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs917154	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs940336	0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[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	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99071200-99091000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr7:99071200-99091600	Weak transcription	Small Intestine	intestine
3	chr7:99071400-99090400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:99071400-99090600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:99071400-99090600	Weak transcription	Right Atrium	heart
6	chr7:99071400-99096200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:99071600-99090400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:99071600-99091200	Weak transcription	Fetal Heart	heart
9	chr7:99071800-99081800	Weak transcription	Pancreas	Pancrea
10	chr7:99071800-99084400	Weak transcription	Fetal Brain Male	brain
11	chr7:99071800-99088600	Weak transcription	Brain Substantia Nigra	brain
12	chr7:99071800-99090400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr7:99071800-99090400	Weak transcription	Brain Angular Gyrus	brain
14	chr7:99071800-99090400	Weak transcription	Psoas Muscle	Psoas
15	chr7:99071800-99090600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:99071800-99091600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr7:99072000-99086400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:99072400-99083600	Weak transcription	Stomach Mucosa	stomach
19	chr7:99072600-99091200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr7:99073200-99082200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:99073600-99084400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:99073800-99083800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:99073800-99085000	Strong transcription	Duodenum Mucosa	Duodenum
24	chr7:99074000-99083600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:99074000-99084600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:99074000-99090400	Weak transcription	Colonic Mucosa	Colon
27	chr7:99074600-99083200	Strong transcription	Dnd41	blood
28	chr7:99075400-99083200	Strong transcription	Fetal Brain Female	brain
29	chr7:99076000-99084400	Weak transcription	Fetal Kidney	kidney
30	chr7:99076600-99085400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:99076600-99090400	Weak transcription	Lung	lung
32	chr7:99076800-99081800	Weak transcription	Gastric	stomach
33	chr7:99076800-99083000	Strong transcription	K562	blood
34	chr7:99076800-99083400	Strong transcription	Fetal Stomach	stomach
35	chr7:99076800-99085200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:99076800-99089800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr7:99076800-99090000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr7:99076800-99090400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:99077000-99084000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr7:99077000-99085200	Strong transcription	Primary T cells from cord blood	blood
41	chr7:99077000-99089800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr7:99077000-99089800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr7:99077000-99090400	Weak transcription	Esophagus	oesophagus
44	chr7:99077000-99090600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr7:99077000-99091200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr7:99077200-99090800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr7:99077200-99091200	Weak transcription	Hela-S3	cervix
48	chr7:99077400-99085000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr7:99077400-99085400	Strong transcription	Fetal Muscle Leg	muscle
50	chr7:99077400-99090000	Weak transcription	Brain Hippocampus Middle	brain

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