Variant report

Variant	rs2353340
Chromosome Location	chr7:11075263-11075264
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	chr7:11012451..11014446-chr7:11075009..11077346,2	MCF-7	breast:
2	chr7:11073711..11075320-chr7:11100379..11102062,2	K562	blood:

Variant related genes	Relation type
ENSG00000106443	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1029583	0.83[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.81[EUR][1000 genomes]
rs1029584	0.83[CEU][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10950334	0.80[ASW][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11975710	0.88[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12669273	0.91[YRI][hapmap]
rs13224675	0.85[ASN][1000 genomes]
rs13232272	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1483201	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1483202	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1483204	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1547944	1.00[JPT][hapmap]
rs1636756	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1640704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1681290	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1681291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17163848	0.87[YRI][hapmap]
rs17346506	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17347241	0.88[ASW][hapmap];0.87[CEU][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs182594	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2110376	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2190293	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs220089	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs220091	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs220094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs220095	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs220096	0.87[EUR][1000 genomes]
rs220097	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2301959	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2353341	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2353342	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2353344	0.96[CEU][hapmap]
rs2625440	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2906564	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2906565	0.88[ASW][hapmap];0.87[CEU][hapmap];0.80[GIH][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2995902	0.89[EUR][1000 genomes]
rs34166672	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34295894	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34665460	0.84[EUR][1000 genomes]
rs35507980	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35580506	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35594158	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35648039	0.83[EUR][1000 genomes]
rs3801435	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3801441	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3801444	0.94[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3801449	0.86[CEU][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs3801450	0.88[ASW][hapmap];0.87[CEU][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes]
rs3801451	0.86[EUR][1000 genomes]
rs4370426	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4720945	0.81[JPT][hapmap]
rs62440480	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6951444	0.81[JPT][hapmap]
rs6969350	0.81[EUR][1000 genomes]
rs7782589	0.88[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7789963	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7791995	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7803348	0.84[EUR][1000 genomes]
rs7806039	0.81[EUR][1000 genomes]
rs9639071	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9768601	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067780	chr7:10649696-11329787	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer 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	29 gene(s)	inside rSNPs	diseases
2	nsv491695	chr7:10649696-11329787	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers 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	29 gene(s)	inside rSNPs	diseases
3	nsv1019888	chr7:10712858-11496785	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1029836	chr7:10713523-11492751	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv538730	chr7:10713523-11492751	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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	31 gene(s)	inside rSNPs	diseases
6	nsv532092	chr7:10731350-11414759	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv887600	chr7:10807685-11090546	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1024171	chr7:10810444-11559156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv949387	chr7:10815994-11281536	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer 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	26 gene(s)	inside rSNPs	diseases
10	nsv1029882	chr7:10872162-11371145	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv817291	chr7:10875417-11562683	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv1031498	chr7:10882696-11110412	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv1030035	chr7:11027819-11256089	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
14	nsv606194	chr7:11042905-11144078	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv887602	chr7:11071993-11220846	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2353340	GLCCI1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:11014600-11092000	Weak transcription	Colonic Mucosa	Colon
2	chr7:11014800-11117400	Weak transcription	HSMMtube	muscle
3	chr7:11015200-11108200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr7:11017200-11076000	Weak transcription	HUVEC	blood vessel
5	chr7:11023200-11076200	Weak transcription	NH-A	brain
6	chr7:11031600-11103800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr7:11035800-11076000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr7:11035800-11092600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:11035800-11113000	Weak transcription	Esophagus	oesophagus
10	chr7:11035800-11113200	Weak transcription	Lung	lung
11	chr7:11035800-11123000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:11036000-11101600	Weak transcription	Placenta	Placenta
13	chr7:11036600-11100800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr7:11039000-11090600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:11039000-11108800	Weak transcription	Psoas Muscle	Psoas
16	chr7:11046000-11128600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr7:11046200-11175000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:11046600-11081200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr7:11046600-11103400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:11046600-11122600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:11046600-11167800	Weak transcription	Thymus	Thymus
22	chr7:11048200-11098600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:11048200-11113400	Weak transcription	Aorta	Aorta
24	chr7:11051000-11076000	Weak transcription	HMEC	breast
25	chr7:11053600-11078000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr7:11054400-11101800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:11054400-11113200	Weak transcription	Pancreas	Pancrea
28	chr7:11054800-11076200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:11055200-11076000	Weak transcription	GM12878-XiMat	blood
30	chr7:11055400-11075800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr7:11055600-11077600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:11056600-11076200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr7:11057800-11190200	Weak transcription	Fetal Brain Male	brain
34	chr7:11064000-11078400	Weak transcription	Brain Angular Gyrus	brain
35	chr7:11064200-11076000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr7:11064200-11076200	Weak transcription	Colon Smooth Muscle	Colon
37	chr7:11064200-11080200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr7:11064200-11093600	Weak transcription	Hela-S3	cervix
39	chr7:11064400-11075400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr7:11064400-11075400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr7:11064400-11076200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr7:11064400-11080600	Weak transcription	Brain Substantia Nigra	brain
43	chr7:11064400-11082800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:11064400-11084800	Weak transcription	Brain Hippocampus Middle	brain
45	chr7:11064400-11088400	Weak transcription	Brain Anterior Caudate	brain
46	chr7:11064400-11104200	Weak transcription	NHEK	skin
47	chr7:11064400-11112400	Weak transcription	Brain Germinal Matrix	brain
48	chr7:11064400-11112400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr7:11064400-11122800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr7:11064600-11075400	Weak transcription	Adipose Nuclei	Adipose

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