Variant report

Variant	rs7643837
Chromosome Location	chr3:141209867-141209868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141208093..141210015-chr3:141222017..141224626,2	MCF-7	breast:
2	chr3:141172850..141174604-chr3:141209853..141211525,2	MCF-7	breast:
3	chr3:141208057..141209932-chr3:141278258..141280316,2	MCF-7	breast:
4	chr3:141209232..141210947-chr3:141248377..141250708,2	K562	blood:
5	chr3:141209148..141211222-chr3:141213660..141216551,2	MCF-7	breast:
6	chr3:141205894..141211656-chr3:141222007..141226023,7	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11711375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11916906	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11917587	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13062809	0.82[EUR][1000 genomes]
rs13069717	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1366042	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1493209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1582875	0.96[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16851435	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs16851438	0.94[JPT][hapmap]
rs16851441	0.88[JPT][hapmap]
rs16851483	0.88[JPT][hapmap]
rs1863867	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2035935	0.88[JPT][hapmap]
rs2035936	0.82[JPT][hapmap]
rs2042864	0.96[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2172471	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2312193	0.92[CEU][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.87[EUR][1000 genomes]
rs2639997	0.88[JPT][hapmap]
rs2639998	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2640017	0.88[JPT][hapmap]
rs295299	0.88[JPT][hapmap]
rs295300	0.81[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap]
rs295320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs295323	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35711802	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732869	0.88[JPT][hapmap]
rs3806646	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3821709	0.88[JPT][hapmap]
rs3821710	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821712	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683610	0.88[JPT][hapmap]
rs6440013	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440015	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6763498	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6767158	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6776003	0.89[CEU][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6785874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6795168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6800122	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612543	0.82[TSI][hapmap]
rs7627807	0.88[JPT][hapmap]
rs7632308	0.92[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9289631	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9813177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850416	0.82[TSI][hapmap]
rs9851256	0.87[CEU][hapmap]
rs9878347	0.94[JPT][hapmap];0.91[YRI][hapmap]
rs9879503	0.94[JPT][hapmap];0.91[YRI][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7643837	GK5	cis	parietal	SCAN
rs7643837	RASA2	cis	cerebellum	SCAN
rs7643837	ZBTB38	cis	cerebellum	SCAN
rs7643837	RASA2	Cis_1M	lymphoblastoid	RTeQTL
rs7643837	RASA2	cis	parietal	SCAN
rs7643837	ATP1B3	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141206800-141217400	Weak transcription	Spleen	Spleen
2	chr3:141207000-141216600	Weak transcription	Small Intestine	intestine
3	chr3:141207000-141217400	Weak transcription	Left Ventricle	heart
4	chr3:141207000-141235800	Weak transcription	Gastric	stomach
5	chr3:141207000-141255000	Weak transcription	Aorta	Aorta
6	chr3:141207200-141217400	Weak transcription	Psoas Muscle	Psoas
7	chr3:141207400-141210000	Weak transcription	NHLF	lung
8	chr3:141207400-141210200	Weak transcription	HSMMtube	muscle
9	chr3:141207400-141210400	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr3:141207400-141211600	Weak transcription	Fetal Brain Male	brain
11	chr3:141207400-141213000	Weak transcription	Brain Angular Gyrus	brain
12	chr3:141207400-141215000	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr3:141207400-141217200	Weak transcription	Fetal Heart	heart
14	chr3:141207400-141217400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:141207400-141217600	Weak transcription	Colonic Mucosa	Colon
16	chr3:141207400-141231400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:141207800-141210400	Enhancers	Primary T cells fromperipheralblood	blood
18	chr3:141207800-141211000	Weak transcription	Fetal Kidney	kidney
19	chr3:141207800-141217400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:141207800-141233200	Weak transcription	Fetal Intestine Large	intestine
21	chr3:141207800-141235600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:141208000-141210000	Weak transcription	A549	lung
23	chr3:141208000-141210200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr3:141208000-141210200	Enhancers	K562	blood
25	chr3:141208000-141210400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:141208000-141210800	Genic enhancers	Primary B cells from cord blood	blood
27	chr3:141208000-141211400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:141208000-141211800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:141208000-141212800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:141208000-141217400	Weak transcription	NHEK	skin
31	chr3:141208200-141210400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr3:141208200-141211000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:141208200-141211600	Enhancers	HUVEC	blood vessel
34	chr3:141208200-141213000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:141208200-141214800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:141208400-141210000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:141208400-141212000	Weak transcription	Ovary	ovary
38	chr3:141208400-141214600	Weak transcription	HSMM	muscle
39	chr3:141208400-141215000	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr3:141208400-141217600	Weak transcription	HMEC	breast
41	chr3:141208400-141231200	Weak transcription	Fetal Lung	lung
42	chr3:141208400-141232600	Weak transcription	NH-A	brain
43	chr3:141208600-141210000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:141208600-141210000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:141208600-141210000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:141208600-141210000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:141208600-141210200	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr3:141208600-141210600	Genic enhancers	Dnd41	blood
49	chr3:141208600-141210600	Weak transcription	HepG2	liver
50	chr3:141208600-141215000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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