Variant report

Variant	rs9663498
Chromosome Location	chr10:61611228-61611229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:61609459..61612041-chr10:61664772..61666784,3	K562	blood:
2	chr10:61611168..61612736-chr10:61629304..61631288,2	K562	blood:
3	chr10:61608407..61613876-chr10:61664743..61669286,7	K562	blood:
4	chr10:61610249..61613076-chr10:61614715..61617033,2	MCF-7	breast:
5	chr10:61604056..61606311-chr10:61608838..61611631,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108091	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10458645	0.85[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10509112	0.82[CHD][hapmap]
rs10761415	0.84[GIH][hapmap]
rs10821604	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10821605	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10821606	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10821607	0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10994026	0.81[JPT][hapmap]
rs10994027	0.81[JPT][hapmap]
rs10994030	0.81[JPT][hapmap]
rs10994031	0.81[JPT][hapmap]
rs10994051	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1171786	0.90[CHD][hapmap]
rs1177701	0.81[CEU][hapmap]
rs12243564	1.00[CEU][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1621496	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1664256	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs1664284	0.95[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs1664285	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs1684901	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs16914233	0.80[JPT][hapmap]
rs1709345	0.83[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871637	0.85[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1871638	0.85[CEU][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2120989	0.82[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs2120990	0.82[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs2458661	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]
rs2458663	0.92[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs3106569	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3793878	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs3844161	0.82[CEU][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3851247	0.91[ASW][hapmap];0.96[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3851248	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3862860	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3862861	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3999569	1.00[CEU][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3999570	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4948244	0.82[CHD][hapmap]
rs4948372	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4948373	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4948374	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4948375	1.00[CEU][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55842846	0.81[ASN][1000 genomes]
rs61848702	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6479653	0.81[JPT][hapmap]
rs6479654	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479661	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6479662	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7068104	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7068247	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7070800	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7074685	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7075215	0.82[GIH][hapmap]
rs7078533	0.82[JPT][hapmap]
rs7079228	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7079588	0.81[JPT][hapmap]
rs7088755	0.81[JPT][hapmap]
rs7088808	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7088886	0.85[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7092259	0.81[JPT][hapmap]
rs7894842	0.84[GIH][hapmap]
rs7908517	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7910256	0.80[JPT][hapmap]
rs7920049	0.80[JPT][hapmap]
rs7920403	0.92[CEU][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9664183	0.92[CEU][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9663498	EGR2	cis	parietal	SCAN
rs9663498	SLC16A9	cis	parietal	SCAN
rs9663498	HOXA4	trans	parietal	SCAN

Chromatin state (count:124 , 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	chr10:61586000-61612200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:61587000-61612000	Weak transcription	Ovary	ovary
12	chr10:61589400-61616200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr10:61591800-61624000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr10:61592600-61616600	Weak transcription	NH-A	brain
15	chr10:61593200-61629400	Weak transcription	Lung	lung
16	chr10:61594000-61614000	Weak transcription	Small Intestine	intestine
17	chr10:61595200-61614000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr10:61595800-61624000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr10:61596000-61612000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr10:61598200-61611800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr10:61598800-61611800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr10:61598800-61614400	Weak transcription	Fetal Brain Female	brain
23	chr10:61599000-61613800	Weak transcription	Aorta	Aorta
24	chr10:61599000-61613800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr10:61599400-61611600	Weak transcription	HMEC	breast
26	chr10:61600000-61616400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr10:61603000-61612400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr10:61603800-61612400	Weak transcription	Brain Hippocampus Middle	brain
29	chr10:61603800-61612600	Weak transcription	Brain Substantia Nigra	brain
30	chr10:61603800-61614200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr10:61603800-61618400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr10:61604200-61611800	Weak transcription	Brain Angular Gyrus	brain
33	chr10:61605200-61612200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr10:61605200-61612400	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr10:61605400-61612000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr10:61605400-61618400	Weak transcription	Fetal Heart	heart
37	chr10:61605600-61611400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr10:61605800-61611400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr10:61606200-61616200	Weak transcription	NHDF-Ad	bronchial
40	chr10:61606600-61612200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr10:61606800-61611600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr10:61606800-61614000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr10:61607200-61612200	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr10:61607600-61611800	Strong transcription	Fetal Lung	lung
45	chr10:61607600-61612200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr10:61607800-61612200	Strong transcription	Dnd41	blood
47	chr10:61607800-61614200	Weak transcription	Stomach Mucosa	stomach
48	chr10:61608000-61611800	Weak transcription	HSMMtube	muscle
49	chr10:61608000-61612400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr10:61608000-61613000	Weak transcription	Psoas Muscle	Psoas

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