Variant report

Variant	rs2458661
Chromosome Location	chr10:61614998-61614999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:61610249..61613076-chr10:61614715..61617033,2	MCF-7	breast:
2	chr10:61612117..61617926-chr10:61664918..61668274,7	MCF-7	breast:
3	chr10:61596064..61599024-chr10:61613612..61615480,2	MCF-7	breast:
4	chr10:61613806..61616077-chr10:61621477..61625736,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108091	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10458645	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10509112	0.85[CHD][hapmap]
rs10761415	0.82[GIH][hapmap]
rs10821604	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10821605	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10821606	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10821607	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10994051	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1149660	0.85[JPT][hapmap]
rs1171786	0.92[CHD][hapmap];0.82[MEX][hapmap]
rs1177701	0.81[CEU][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs12243564	1.00[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1621496	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs1664256	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs1664284	0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs1664285	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1684901	0.85[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1709342	0.85[JPT][hapmap]
rs1709343	0.85[JPT][hapmap]
rs1709345	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871637	0.85[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1871638	0.85[CEU][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2120989	0.82[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2120990	0.82[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs2271562	0.83[JPT][hapmap]
rs2440926	0.85[JPT][hapmap]
rs2458663	0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs3106569	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3793878	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs3844161	0.82[CEU][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3851247	0.91[ASW][hapmap];0.96[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3851248	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3862860	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3862861	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3999569	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3999570	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4948244	0.84[CHD][hapmap]
rs4948372	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4948373	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4948374	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4948375	1.00[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55842846	0.81[ASN][1000 genomes]
rs61848702	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6479654	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479661	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6479662	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7068104	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7068247	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7070800	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7074685	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7075215	0.80[GIH][hapmap]
rs7079228	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7088808	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7088886	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.91[ASN][1000 genomes]
rs7894842	0.82[GIH][hapmap]
rs7908517	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7920403	0.92[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9663498	0.91[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9664183	0.92[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2458661	SLC16A9	cis	parietal	SCAN
rs2458661	HOXA4	trans	parietal	SCAN
rs2458661	EGR2	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61571400-61628000	Weak transcription	Spleen	Spleen
2	chr10:61571600-61616000	Weak transcription	Fetal Kidney	kidney
3	chr10:61572000-61615000	Weak transcription	Colonic Mucosa	Colon
4	chr10:61572400-61618800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr10:61578000-61623200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr10:61580200-61624200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr10:61580400-61624200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr10:61580600-61616200	Weak transcription	Fetal Brain Male	brain
9	chr10:61583200-61640600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:61589400-61616200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:61591800-61624000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr10:61592600-61616600	Weak transcription	NH-A	brain
13	chr10:61593200-61629400	Weak transcription	Lung	lung
14	chr10:61595800-61624000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr10:61600000-61616400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr10:61603800-61618400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr10:61605400-61618400	Weak transcription	Fetal Heart	heart
18	chr10:61606200-61616200	Weak transcription	NHDF-Ad	bronchial
19	chr10:61608000-61615000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr10:61608000-61615600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:61608000-61617800	Weak transcription	Pancreas	Pancrea
22	chr10:61608000-61618200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr10:61608000-61624000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr10:61608000-61624200	Weak transcription	Right Ventricle	heart
25	chr10:61608000-61637200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr10:61609200-61616200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr10:61609200-61617800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr10:61609400-61615600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr10:61609600-61616200	Weak transcription	HSMM	muscle
30	chr10:61609800-61617000	Weak transcription	Osteobl	bone
31	chr10:61610000-61616600	Weak transcription	NHLF	lung
32	chr10:61610000-61619600	Weak transcription	Fetal Muscle Leg	muscle
33	chr10:61610000-61624200	Weak transcription	Fetal Thymus	thymus
34	chr10:61610200-61618400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr10:61610200-61624000	Weak transcription	Hela-S3	cervix
36	chr10:61610200-61624400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr10:61610400-61617600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr10:61610400-61619800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr10:61610400-61624200	Weak transcription	Thymus	Thymus
40	chr10:61610400-61624400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr10:61610400-61628000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr10:61610600-61615800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:61610800-61624400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr10:61611800-61618000	Enhancers	Brain Anterior Caudate	brain
45	chr10:61612000-61616600	Enhancers	Colon Smooth Muscle	Colon
46	chr10:61612000-61624000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr10:61612000-61624000	Weak transcription	HMEC	breast
48	chr10:61612200-61615000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr10:61612200-61616600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr10:61612200-61622200	Weak transcription	Dnd41	blood

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