Variant report

Variant	rs2950387
Chromosome Location	chr12:57021006-57021007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56988153..56991262-chr12:57020461..57022957,3	MCF-7	breast:
2	chr12:56995073..56997290-chr12:57020489..57023274,4	MCF-7	breast:
3	chr12:57002945..57005417-chr12:57018458..57021236,3	K562	blood:
4	chr12:57014744..57016426-chr12:57019361..57021308,2	K562	blood:
5	chr12:57002945..57004692-chr12:57018540..57021236,2	K562	blood:

Variant related genes	Relation type
ENSG00000076108	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1020848	0.93[ASN][1000 genomes]
rs1026565	0.84[TSI][hapmap]
rs10450	0.80[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10747769	0.88[ASN][1000 genomes]
rs10783794	0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs10876913	0.91[ASN][1000 genomes]
rs10876914	0.93[ASN][1000 genomes]
rs10876915	0.93[ASN][1000 genomes]
rs10876916	0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1107479	0.87[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11171914	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11171916	0.93[ASN][1000 genomes]
rs11171917	0.93[ASN][1000 genomes]
rs11171951	0.80[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs11835120	0.93[ASN][1000 genomes]
rs11837319	0.93[ASN][1000 genomes]
rs12229457	0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1465081	0.93[ASN][1000 genomes]
rs1466382	0.80[CHB][hapmap]
rs1563896	0.80[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1563897	0.80[ASN][1000 genomes]
rs1962963	0.81[ASN][1000 genomes]
rs1979325	0.80[CHB][hapmap]
rs2035081	0.86[TSI][hapmap]
rs2242497	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2255074	0.87[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2256341	0.82[ASN][1000 genomes]
rs2290893	0.87[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs2290894	0.80[CHB][hapmap]
rs2926740	0.93[ASN][1000 genomes]
rs2926743	0.80[CHB][hapmap]
rs2950388	0.93[ASN][1000 genomes]
rs2950389	0.90[JPT][hapmap]
rs2950390	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[ASN][1000 genomes]
rs2950393	0.93[ASN][1000 genomes]
rs2950394	0.93[ASN][1000 genomes]
rs2958123	0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2958124	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2958127	0.80[CHB][hapmap];0.86[TSI][hapmap]
rs2958130	0.80[CHB][hapmap];0.86[TSI][hapmap]
rs2958139	0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs2958145	0.93[ASN][1000 genomes]
rs2958146	0.93[ASN][1000 genomes]
rs2958153	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2958154	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[ASN][1000 genomes]
rs2958155	0.87[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[ASN][1000 genomes]
rs3214051	0.80[CHB][hapmap];0.82[TSI][hapmap]
rs36012661	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4759028	0.84[ASN][1000 genomes]
rs4759254	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs67046307	0.93[ASN][1000 genomes]
rs7297289	0.86[ASN][1000 genomes]
rs7303216	0.86[ASN][1000 genomes]
rs7313074	0.80[CHB][hapmap]
rs7315472	0.93[ASN][1000 genomes]
rs73337030	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7967600	0.80[CHB][hapmap];0.82[TSI][hapmap]
rs7972420	0.89[ASN][1000 genomes]
rs7973157	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7973618	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7975783	0.87[ASN][1000 genomes]
rs7978685	0.80[CHB][hapmap]
rs7980317	0.80[CHB][hapmap];0.82[TSI][hapmap]
rs7980378	0.88[ASN][1000 genomes]
rs7980835	0.90[ASN][1000 genomes]
rs898609	0.80[CHB][hapmap]
rs898611	0.80[CHB][hapmap];0.82[TSI][hapmap]
rs9368	1.00[ASW][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs941207	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs941209	0.84[JPT][hapmap]
rs9634246	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9634247	0.91[ASN][1000 genomes]
rs9634277	0.91[ASN][1000 genomes]
rs9989034	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2950387	HOXC6	cis	cerebellum	SCAN
rs2950387	LETMD1	cis	cerebellum	SCAN
rs2950387	HSD17B6	cis	cerebellum	SCAN
rs2950387	IL23A	cis	cerebellum	SCAN
rs2950387	STAT6	cis	parietal	SCAN
rs2950387	RAB5B	cis	cerebellum	SCAN
rs2950387	PRIM1	cis	cerebellum	SCAN
rs2950387	OR10A7	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56988400-57021600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:56988800-57021600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:56991000-57022000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:56994200-57021200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:56995000-57021400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:57009800-57022200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:57010400-57022200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:57010800-57022000	Weak transcription	Small Intestine	intestine
9	chr12:57011000-57021400	Weak transcription	Fetal Brain Male	brain
10	chr12:57011400-57022000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:57011400-57022000	Weak transcription	Brain Germinal Matrix	brain
12	chr12:57011400-57022200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:57011400-57022200	Weak transcription	Colonic Mucosa	Colon
14	chr12:57011400-57022200	Weak transcription	Stomach Mucosa	stomach
15	chr12:57011400-57022400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:57011400-57022400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:57011400-57022400	Weak transcription	Aorta	Aorta
18	chr12:57011400-57022400	Weak transcription	Gastric	stomach
19	chr12:57011400-57022600	Weak transcription	Esophagus	oesophagus
20	chr12:57011800-57021800	Strong transcription	Fetal Thymus	thymus
21	chr12:57011800-57022200	Weak transcription	Fetal Brain Female	brain
22	chr12:57015000-57022000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:57015200-57022000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:57015400-57022200	Weak transcription	Fetal Kidney	kidney
25	chr12:57015600-57022000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:57015600-57022200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:57016800-57022000	Weak transcription	HUVEC	blood vessel
28	chr12:57017600-57022000	Weak transcription	HSMMtube	muscle
29	chr12:57017600-57022200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:57017600-57022200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:57017800-57022200	Weak transcription	Left Ventricle	heart
32	chr12:57017800-57022400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:57018000-57021200	Weak transcription	Ovary	ovary
34	chr12:57018000-57021400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:57018000-57022000	Weak transcription	Psoas Muscle	Psoas
36	chr12:57018000-57022200	Weak transcription	Right Ventricle	heart
37	chr12:57018200-57022000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr12:57018200-57022200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:57018200-57022400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:57018200-57022600	Weak transcription	Spleen	Spleen
41	chr12:57018400-57022000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:57018400-57022200	Weak transcription	Brain Anterior Caudate	brain
43	chr12:57018400-57022200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr12:57018600-57022000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:57018800-57022000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr12:57018800-57022000	Weak transcription	Hela-S3	cervix
47	chr12:57019200-57021600	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr12:57019200-57022200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr12:57019800-57021200	Strong transcription	Placenta	Placenta
50	chr12:57019800-57021400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links