Variant report

Variant	rs10232457
Chromosome Location	chr7:87462515-87462516
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:87462306..87463963-chr7:87471322..87473342,2	K562	blood:
2	chr7:87458484..87460611-chr7:87462209..87463941,2	K562	blood:
3	chr7:87460038..87462907-chr7:87508297..87510823,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075303	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1015415	1.00[CEU][hapmap]
rs10215700	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10215973	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10226830	0.86[EUR][1000 genomes]
rs10226849	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10227951	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10230718	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10237097	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10237201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10238564	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10239908	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10239922	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10244734	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10245767	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10246786	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10247258	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10252990	1.00[CEU][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253106	1.00[ASW][hapmap];0.86[CEU][hapmap];0.88[GIH][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259182	0.95[EUR][1000 genomes]
rs10260007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264856	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10268868	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10269158	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10276499	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10276819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10952899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12532279	0.95[EUR][1000 genomes]
rs12532941	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12533477	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12539395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12540032	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12540931	1.00[CEU][hapmap]
rs12669619	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13438651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17149864	1.00[CEU][hapmap];0.90[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[EUR][1000 genomes]
rs17150009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2073985	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2106522	0.91[EUR][1000 genomes]
rs2157926	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2157929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2188527	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2188828	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2214101	1.00[CEU][hapmap];0.90[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2214106	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2285646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285649	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2373574	0.93[EUR][1000 genomes]
rs28437979	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28449219	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28449354	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28537604	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28546778	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28627774	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28642834	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28645115	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28774398	0.95[EUR][1000 genomes]
rs28831998	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58638862	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59058733	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6465117	0.91[EUR][1000 genomes]
rs6465118	0.87[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs6948061	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6951067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6952943	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6972098	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73706914	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73706916	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73706922	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73706924	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73706950	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7790722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7798074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9655954	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9655955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs976602	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs992422	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1015862	chr7:87075394-88049798	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1023352	chr7:87418818-88192925	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv539005	chr7:87418818-88192925	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv967463	chr7:87461803-87465302	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10232457	G0S2	trans	brain	seeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:87455000-87474200	Weak transcription	Left Ventricle	heart
2	chr7:87455200-87473000	Weak transcription	Liver	Liver
3	chr7:87455200-87486600	Weak transcription	Brain Germinal Matrix	brain
4	chr7:87455400-87474200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr7:87457400-87474200	Weak transcription	Aorta	Aorta
6	chr7:87457800-87474200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:87458200-87478400	Weak transcription	Adipose Nuclei	Adipose
8	chr7:87458400-87478600	Weak transcription	Brain Anterior Caudate	brain
9	chr7:87458600-87469400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:87458600-87474400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr7:87458600-87480400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:87458800-87467600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr7:87459000-87466400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr7:87459000-87474200	Weak transcription	Primary B cells from cord blood	blood
15	chr7:87459000-87474400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr7:87459200-87482400	Weak transcription	A549	lung
17	chr7:87459400-87464800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:87459400-87474200	Weak transcription	Fetal Stomach	stomach
19	chr7:87459400-87474400	Weak transcription	HUVEC	blood vessel
20	chr7:87459600-87471600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr7:87459600-87473200	Weak transcription	Fetal Thymus	thymus
22	chr7:87459600-87474200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:87459600-87474600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:87459600-87474600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr7:87459800-87464800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:87459800-87474800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:87459800-87478600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr7:87459800-87480600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr7:87460000-87464600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr7:87460000-87474400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:87460000-87474400	Weak transcription	Fetal Brain Female	brain
32	chr7:87460200-87466800	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr7:87460200-87471800	Weak transcription	Fetal Brain Male	brain
34	chr7:87460200-87478800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:87460400-87487200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr7:87460600-87463200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr7:87460600-87463600	Strong transcription	Dnd41	blood
38	chr7:87460600-87466800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:87460600-87474400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr7:87460600-87474400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr7:87460600-87481200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr7:87460600-87481600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr7:87460600-87498000	Weak transcription	Fetal Heart	heart
44	chr7:87460800-87462800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:87460800-87474400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr7:87461000-87463000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr7:87461000-87471400	Weak transcription	GM12878-XiMat	blood
48	chr7:87461000-87473400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr7:87461200-87471600	Weak transcription	K562	blood
50	chr7:87461200-87474200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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