Variant report

Variant	rs2915872
Chromosome Location	chr5:151157572-151157573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:151157144..151159075-chr5:151199761..151202393,2	MCF-7	breast:

Extended variants
information (count: 123 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10044368	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10065313	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10075101	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1042877	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10476776	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10476778	0.85[EUR][1000 genomes]
rs1062177	0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[ASN][1000 genomes]
rs11167557	0.84[EUR][1000 genomes]
rs11954338	0.86[EUR][1000 genomes]
rs12108921	0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs12109022	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12654877	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12658422	0.84[EUR][1000 genomes]
rs1433041	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1549920	0.94[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs1549921	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17741826	0.94[CHB][hapmap]
rs17804178	0.83[ASN][1000 genomes]
rs1972780	0.81[ASN][1000 genomes]
rs1978710	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2016409	0.82[ASN][1000 genomes]
rs2053063	0.83[ASN][1000 genomes]
rs2347596	0.83[ASN][1000 genomes]
rs2347597	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2913889	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs2913892	0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs2913893	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2913894	0.92[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs2915815	0.81[ASN][1000 genomes]
rs2915816	0.89[ASN][1000 genomes]
rs2915817	0.81[ASN][1000 genomes]
rs2915818	0.81[ASN][1000 genomes]
rs2915821	0.84[ASN][1000 genomes]
rs2915822	0.94[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs2915823	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915824	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915826	0.94[CHB][hapmap]
rs2915827	0.94[CHB][hapmap]
rs2915828	0.80[ASN][1000 genomes]
rs2915829	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2915868	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915869	0.83[ASN][1000 genomes]
rs2915870	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915871	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915873	0.84[ASN][1000 genomes]
rs2915874	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2915876	0.94[CHB][hapmap];0.88[CHD][hapmap]
rs2915878	0.94[CHB][hapmap]
rs2915879	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs2915880	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs2915881	0.82[ASN][1000 genomes]
rs2915882	0.82[ASN][1000 genomes]
rs2915883	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915885	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2915886	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2915887	0.81[ASN][1000 genomes]
rs2915888	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2915890	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2915891	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915892	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915893	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2915894	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964568	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2964569	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2964570	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964571	0.83[ASN][1000 genomes]
rs2964572	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964573	0.83[ASN][1000 genomes]
rs2964574	0.94[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs2964577	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2964578	0.82[ASN][1000 genomes]
rs2964580	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964581	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2964582	0.82[ASN][1000 genomes]
rs2964584	0.94[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs2964585	0.83[ASN][1000 genomes]
rs2964587	0.94[CHB][hapmap]
rs2964588	0.80[ASN][1000 genomes]
rs2964589	0.80[ASN][1000 genomes]
rs2964590	0.80[ASN][1000 genomes]
rs2964591	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs2964592	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs2964593	0.80[ASN][1000 genomes]
rs2964610	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2964611	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2964612	0.82[ASN][1000 genomes]
rs2964613	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35692301	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4360031	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4362933	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4379180	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4419575	0.86[EUR][1000 genomes]
rs4472253	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4510568	0.86[EUR][1000 genomes]
rs4541649	0.85[EUR][1000 genomes]
rs4555782	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4571461	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4594844	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4629583	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4629586	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62394144	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6579897	0.94[CHB][hapmap]
rs6579906	0.85[EUR][1000 genomes]
rs6579908	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6579909	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6579910	0.82[AMR][1000 genomes]
rs6863833	0.84[EUR][1000 genomes]
rs6863837	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6879461	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72802204	0.83[ASN][1000 genomes]
rs7341167	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7702751	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7715560	0.82[AMR][1000 genomes]
rs7715874	0.81[EUR][1000 genomes]
rs7719617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs7720579	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7728956	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7733241	0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7734314	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7735811	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs892005	0.83[ASN][1000 genomes]
rs892006	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs973529	0.83[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2915872	C5orf46	cis	parietal	SCAN
rs2915872	SYNPO	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:151152800-151160000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:151152800-151163000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:151153000-151160000	Weak transcription	Gastric	stomach
4	chr5:151153000-151167400	Weak transcription	Esophagus	oesophagus
5	chr5:151153000-151167400	Weak transcription	Lung	lung
6	chr5:151153000-151167600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:151153800-151160400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:151153800-151162000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr5:151153800-151165200	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr5:151153800-151166800	Weak transcription	Colonic Mucosa	Colon
11	chr5:151153800-151167400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:151153800-151169800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:151154000-151157600	Enhancers	Colon Smooth Muscle	Colon
14	chr5:151154000-151157600	Enhancers	Fetal Heart	heart
15	chr5:151154000-151158000	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr5:151154400-151168800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:151154400-151169000	Weak transcription	HSMMtube	muscle
18	chr5:151154600-151168800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:151154800-151158600	Weak transcription	Stomach Mucosa	stomach
20	chr5:151154800-151165000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr5:151155000-151158200	Weak transcription	Primary B cells from cord blood	blood
22	chr5:151155200-151157600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:151155200-151158400	Weak transcription	Fetal Intestine Large	intestine
24	chr5:151155200-151159600	Genic enhancers	Hela-S3	cervix
25	chr5:151155200-151160600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr5:151155200-151163600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:151155200-151167600	Weak transcription	Spleen	Spleen
28	chr5:151155400-151157600	Genic enhancers	A549	lung
29	chr5:151155400-151158400	Weak transcription	Pancreas	Pancrea
30	chr5:151155400-151158800	Weak transcription	Fetal Brain Female	brain
31	chr5:151155400-151160600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:151155600-151157800	Strong transcription	Fetal Kidney	kidney
33	chr5:151155600-151158600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr5:151155800-151158000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:151155800-151158000	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr5:151155800-151158000	Strong transcription	NHDF-Ad	bronchial
37	chr5:151155800-151158200	Strong transcription	NHEK	skin
38	chr5:151155800-151158800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:151155800-151159000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr5:151155800-151159200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr5:151155800-151159200	Genic enhancers	HepG2	liver
42	chr5:151155800-151159400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:151155800-151163800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:151155800-151167400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr5:151155800-151172200	Weak transcription	Aorta	Aorta
46	chr5:151155800-151177000	Weak transcription	Fetal Brain Male	brain
47	chr5:151156000-151157600	Genic enhancers	Dnd41	blood
48	chr5:151156000-151158000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:151156000-151158800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr5:151156000-151159400	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links