Variant report

Variant	rs2458663
Chromosome Location	chr10:61623888-61623889
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:61622142..61625052-chr10:61830945..61832691,2	K562	blood:
2	chr10:61619348..61621030-chr10:61622725..61624454,2	K562	blood:
3	chr10:61613806..61616077-chr10:61621477..61625736,3	MCF-7	breast:
4	chr10:61623049..61625625-chr10:61665544..61668318,6	MCF-7	breast:
5	chr10:61623680..61630815-chr10:61664299..61668134,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108091	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10458645	0.90[CHD][hapmap];0.90[JPT][hapmap]
rs10821604	0.90[JPT][hapmap]
rs10821607	0.90[JPT][hapmap]
rs10994022	0.82[JPT][hapmap]
rs10994026	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs10994027	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs10994030	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10994031	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs10994051	0.97[ASN][1000 genomes]
rs1149660	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1149661	0.85[ASN][1000 genomes]
rs1149662	0.85[ASN][1000 genomes]
rs1149663	0.85[ASN][1000 genomes]
rs1171786	0.94[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs1171788	0.92[ASN][1000 genomes]
rs12243564	0.94[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.89[ASN][1000 genomes]
rs12244844	0.80[ASN][1000 genomes]
rs12252428	0.81[ASN][1000 genomes]
rs12266466	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1621496	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1664255	0.93[ASN][1000 genomes]
rs1664256	0.94[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[ASN][1000 genomes]
rs1664284	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1664285	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1684896	0.93[ASN][1000 genomes]
rs1684901	0.90[JPT][hapmap]
rs1684929	0.85[ASN][1000 genomes]
rs16914233	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1709342	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1709343	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1709344	0.86[ASN][1000 genomes]
rs1709345	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1871637	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1871638	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2120989	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2120990	0.89[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2271562	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs2440926	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2458661	0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs2458664	0.85[ASN][1000 genomes]
rs3106569	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3844161	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3851247	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.97[ASN][1000 genomes]
rs3851248	0.97[ASN][1000 genomes]
rs3862860	0.97[ASN][1000 genomes]
rs3862861	0.97[ASN][1000 genomes]
rs3999569	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3999570	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[ASN][1000 genomes]
rs4948372	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[ASN][1000 genomes]
rs4948373	0.97[ASN][1000 genomes]
rs4948374	0.95[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.84[ASN][1000 genomes]
rs4948375	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs55706286	0.80[ASN][1000 genomes]
rs55842846	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57348988	0.81[ASN][1000 genomes]
rs61848702	0.98[ASN][1000 genomes]
rs6479653	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs6479654	0.90[JPT][hapmap]
rs6479657	0.89[ASN][1000 genomes]
rs6479658	0.82[ASN][1000 genomes]
rs6479659	0.93[ASN][1000 genomes]
rs6479660	0.92[ASN][1000 genomes]
rs6479661	0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6479662	0.97[ASN][1000 genomes]
rs7068104	0.94[ASN][1000 genomes]
rs7068247	0.97[ASN][1000 genomes]
rs7070800	0.95[ASN][1000 genomes]
rs7074685	0.97[ASN][1000 genomes]
rs7078533	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7079228	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs7079588	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs7080447	0.82[ASN][1000 genomes]
rs7088755	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7088808	0.97[ASN][1000 genomes]
rs7088886	0.90[CHD][hapmap];0.90[JPT][hapmap]
rs7092259	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs72817923	0.80[ASN][1000 genomes]
rs7908517	0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7910256	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7920049	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7920403	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9663498	0.92[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs9664183	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2458663	EGR2	cis	parietal	SCAN
rs2458663	CCDC6	cis	Esophagus Mucosa	GTEx
rs2458663	SLC16A9	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:61571400-61628000	Weak transcription	Spleen	Spleen
2	chr10:61580200-61624200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr10:61580400-61624200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr10:61583200-61640600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr10:61591800-61624000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr10:61593200-61629400	Weak transcription	Lung	lung
7	chr10:61595800-61624000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:61608000-61624000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr10:61608000-61624200	Weak transcription	Right Ventricle	heart
10	chr10:61608000-61637200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:61610000-61624200	Weak transcription	Fetal Thymus	thymus
12	chr10:61610200-61624000	Weak transcription	Hela-S3	cervix
13	chr10:61610200-61624400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr10:61610400-61624200	Weak transcription	Thymus	Thymus
15	chr10:61610400-61624400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr10:61610400-61628000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr10:61610800-61624400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr10:61612000-61624000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr10:61612000-61624000	Weak transcription	HMEC	breast
20	chr10:61612200-61624800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr10:61612400-61624400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr10:61613200-61624200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr10:61613200-61624200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr10:61613600-61624200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr10:61614200-61629400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr10:61614400-61624200	Weak transcription	Brain Angular Gyrus	brain
27	chr10:61614600-61624400	Weak transcription	Gastric	stomach
28	chr10:61614800-61624200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr10:61614800-61624200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr10:61615200-61628000	Weak transcription	Esophagus	oesophagus
31	chr10:61616000-61624200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:61616000-61624400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr10:61616400-61624000	Weak transcription	Small Intestine	intestine
34	chr10:61616600-61626600	Weak transcription	Aorta	Aorta
35	chr10:61618000-61624000	Weak transcription	Brain Anterior Caudate	brain
36	chr10:61618000-61632600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr10:61618400-61624400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr10:61618400-61628600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr10:61618600-61624000	Weak transcription	Right Atrium	heart
40	chr10:61618600-61624000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr10:61618600-61624800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr10:61618600-61633200	Weak transcription	HSMM	muscle
43	chr10:61618800-61624200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr10:61618800-61624200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr10:61618800-61624200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr10:61618800-61624200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr10:61618800-61624200	Weak transcription	Ovary	ovary
48	chr10:61618800-61625000	Weak transcription	NHDF-Ad	bronchial
49	chr10:61618800-61625200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr10:61619000-61624000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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