Variant report

Variant	rs2034651
Chromosome Location	chr15:40802446-40802447
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40768341..40769878-chr15:40802336..40804015,2	MCF-7	breast:
2	chr15:40761396..40764374-chr15:40800140..40802676,2	K562	blood:
3	chr15:40730812..40737363-chr15:40801226..40806622,9	K562	blood:
4	chr15:40763028..40765683-chr15:40802404..40803926,2	MCF-7	breast:
5	chr15:40800305..40802269-chr15:40802285..40805070,2	K562	blood:
6	chr15:40801534..40804191-chr15:40830855..40832642,2	K562	blood:

Variant related genes	Relation type
ENSG00000140320	Chromatin interaction
ENSG00000169105	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 36 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11070275	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070277	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11070285	0.92[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs11070286	0.92[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs11632061	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11632370	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11638742	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11639464	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11852694	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs11854986	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs11855334	0.92[CEU][hapmap];0.83[CHD][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs11855923	0.92[CEU][hapmap]
rs11856438	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs11856802	0.96[CEU][hapmap];0.80[CHB][hapmap]
rs11858113	0.92[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs12594548	0.96[CEU][hapmap];0.81[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12595610	0.96[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12905162	0.92[CEU][hapmap]
rs12914743	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs12916042	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16970851	0.92[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs1806961	0.96[EUR][1000 genomes]
rs1811513	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1813898	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1869301	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1869302	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1993212	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2034652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167795	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412531	0.92[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2412532	0.91[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2412534	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2412544	0.92[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs2444302	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2924386	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2924388	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2959536	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2959545	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3092979	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs35047458	0.92[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs3751653	0.92[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs4923875	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4923876	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4924472	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924478	0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4924479	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4924480	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4924481	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs588686	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs590046	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs603623	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs616937	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs618399	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs619711	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs620198	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6492947	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs6492951	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs654317	0.89[EUR][1000 genomes]
rs6582	0.88[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7178756	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7183273	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7494968	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8026605	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs8029384	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8034326	0.81[EUR][1000 genomes]
rs8038407	0.80[EUR][1000 genomes]
rs8041534	0.92[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs896795	0.92[CEU][hapmap];0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9652415	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs976401	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:36)

SNP	Gene	Cis/trans	Tissue	Source
rs2034651	C15orf57	cis	Esophagus Mucosa	GTEx
rs2034651	MRPL42P5	cis	multi-tissue	Pritchard
rs2034651	MRPL42P5	cis	lymphoblastoid	seeQTL
rs2034651	CCDC32	cis	multi-tissue	Pritchard
rs2034651	ZFYVE19	cis	parietal	SCAN
rs2034651	C15orf57	cis	Artery Tibial	GTEx
rs2034651	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs2034651	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs2034651	C15orf57	cis	lymphoblastoid	seeQTL
rs2034651	C15orf57	cis	Lymphoblastoid	GTEx
rs2034651	C15orf57	cis	Cerebellum	GTEx
rs2034651	C15orf57	cis	Artery Aorta	GTEx
rs2034651	ITPKA	cis	parietal	SCAN
rs2034651	IVD	cis	cerebellum	SCAN
rs2034651	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs2034651	C15orf57	cis	cerebellum	SCAN
rs2034651	C15orf57	cis	Nerve Tibial	GTEx
rs2034651	C15orf57	cis	Adipose Subcutaneous	GTEx
rs2034651	RP11-111A22.1	cis	Artery Aorta	GTEx
rs2034651	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs2034651	RP11-111A22.1	cis	Artery Tibial	GTEx
rs2034651	CCDC32	cis	normal skin	skin_eQTL
rs2034651	CCDC32	cis	lesional skin	skin_eQTL
rs2034651	C15orf57	cis	Esophagus Muscularis	GTEx
rs2034651	C15orf57	cis	lung	GTEx
rs2034651	LPCAT4	cis	parietal	SCAN
rs2034651	C15orf23	cis	cerebellum	SCAN
rs2034651	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs2034651	C15orf57	cis	Heart Left Ventricle	GTEx
rs2034651	PLA2G4E	cis	parietal	SCAN
rs2034651	C15orf57	cis	Muscle Skeletal	GTEx
rs2034651	DISP2	cis	parietal	SCAN
rs2034651	ZFYVE19	cis	cerebellum	SCAN
rs2034651	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs2034651	C15orf57	cis	parietal	SCAN
rs2034651	RP11-111A22.1	cis	lung	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40799200-40803200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:40799600-40802800	Weak transcription	Spleen	Spleen
3	chr15:40799800-40802600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:40799800-40802600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr15:40799800-40802800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:40799800-40802800	Weak transcription	Liver	Liver
7	chr15:40799800-40802800	Weak transcription	Brain Anterior Caudate	brain
8	chr15:40799800-40802800	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:40799800-40802800	Weak transcription	Left Ventricle	heart
10	chr15:40799800-40802800	Weak transcription	Psoas Muscle	Psoas
11	chr15:40799800-40803000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:40799800-40803000	Weak transcription	Ovary	ovary
13	chr15:40799800-40803000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:40799800-40803200	Weak transcription	Brain Substantia Nigra	brain
15	chr15:40799800-40803200	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:40799800-40803200	Weak transcription	Pancreas	Pancrea
17	chr15:40799800-40803200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:40799800-40803200	Weak transcription	HMEC	breast
19	chr15:40799800-40803400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:40799800-40803400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:40799800-40803400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:40799800-40803400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr15:40799800-40803400	Weak transcription	Right Atrium	heart
24	chr15:40800000-40802800	Weak transcription	K562	blood
25	chr15:40800000-40803600	Weak transcription	A549	lung
26	chr15:40801000-40803400	Enhancers	Placenta	Placenta
27	chr15:40802400-40802600	Enhancers	Right Ventricle	heart
28	chr15:40802400-40802800	Bivalent Enhancer	GM12878-XiMat	blood
29	chr15:40802400-40803200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links