Variant report

Variant	rs3898937
Chromosome Location	chr12:75947644-75947645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75946731..75948885-chr12:75954512..75956708,2	MCF-7	breast:
2	chr12:75942170..75945016-chr12:75945671..75947951,2	MCF-7	breast:
3	chr12:75942788..75945762-chr12:75947332..75949083,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10748282	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10785195	0.83[EUR][1000 genomes]
rs10785198	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10879929	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10879930	0.83[EUR][1000 genomes]
rs10879932	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10879933	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10879934	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10879935	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10879936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10879938	0.89[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs10879945	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs11180562	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180575	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180584	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11180598	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11180603	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11495681	0.80[EUR][1000 genomes]
rs11514051	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11519910	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11520226	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12811250	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1480005	0.80[EUR][1000 genomes]
rs1697759	0.83[EUR][1000 genomes]
rs17115238	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2054518	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2366988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2366989	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2886826	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34406885	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3847671	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4323912	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4882631	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58886425	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60465677	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6582293	0.88[EUR][1000 genomes]
rs7137366	0.81[CEU][hapmap]
rs7137610	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes]
rs7300994	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7305673	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs7314220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs733880	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs733881	0.89[CEU][hapmap];0.95[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs7955264	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7956673	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes]
rs7956799	0.82[EUR][1000 genomes]
rs7956953	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7958508	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7962144	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs7962276	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs7979460	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7979600	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7980713	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9634253	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs3898937	GLIPR1	cis	cerebellum	SCAN
rs3898937	GLIPR1L2	cis	Thyroid	GTEx
rs3898937	GLIPR1L2	cis	Nerve Tibial	GTEx
rs3898937	RP11-585P4.5	cis	Artery Tibial	GTEx
rs3898937	GLIPR1L2	cis	Esophagus Mucosa	GTEx
rs3898937	GLIPR1L2	cis	parietal	SCAN
rs3898937	GLIPR1L2	cis	lung	GTEx
rs3898937	GLIPR1L2	cis	Artery Tibial	GTEx
rs3898937	KRR1	cis	cerebellum	SCAN
rs3898937	KRR1	cis	parietal	SCAN
rs3898937	RP11-585P4.5	cis	Esophagus Muscularis	GTEx
rs3898937	RP11-585P4.5	cis	Esophagus Mucosa	GTEx
rs3898937	GLIPR1L1	cis	multi-tissue	Pritchard
rs3898937	GLIPR1L1	cis	lymphoblastoid	seeQTL
rs3898937	RP11-585P4.5	cis	Adipose Subcutaneous	GTEx
rs3898937	GLIPR1	cis	parietal	SCAN
rs3898937	GLIPR1L2	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75944800-75948200	Weak transcription	Lung	lung
2	chr12:75944800-75948200	Weak transcription	Right Atrium	heart
3	chr12:75944800-75954000	Weak transcription	Pancreas	Pancrea
4	chr12:75945400-75948800	Enhancers	Fetal Heart	heart
5	chr12:75946600-75957600	Weak transcription	Fetal Brain Male	brain
6	chr12:75946800-75947800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:75946800-75948200	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr12:75947000-75948000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr12:75947000-75948600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:75947200-75947800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:75947200-75947800	Enhancers	H9 Cell Line	embryonic stem cell
12	chr12:75947200-75947800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr12:75947200-75947800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:75947200-75947800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:75947200-75947800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:75947200-75948000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:75947200-75948000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr12:75947200-75948200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:75947200-75948400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:75947200-75948400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr12:75947200-75948400	Enhancers	Fetal Lung	lung
22	chr12:75947200-75948400	Enhancers	HMEC	breast
23	chr12:75947200-75948600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr12:75947200-75948600	Enhancers	Fetal Muscle Leg	muscle
25	chr12:75947200-75948600	Enhancers	Dnd41	blood
26	chr12:75947200-75948600	Enhancers	NH-A	brain
27	chr12:75947200-75948800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:75947200-75948800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:75947200-75948800	Enhancers	Osteobl	bone
30	chr12:75947200-75949000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:75947200-75949000	Enhancers	NHDF-Ad	bronchial
32	chr12:75947400-75947800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:75947400-75947800	Enhancers	Fetal Kidney	kidney
34	chr12:75947400-75947800	Flanking Active TSS	HSMMtube	muscle
35	chr12:75947400-75948000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:75947400-75948000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr12:75947400-75948200	Enhancers	Adipose Nuclei	Adipose
38	chr12:75947400-75948400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:75947400-75948400	Enhancers	A549	lung
40	chr12:75947400-75948400	Enhancers	HSMM	muscle
41	chr12:75947400-75948400	Enhancers	NHLF	lung
42	chr12:75947400-75948800	Enhancers	Rectal Smooth Muscle	rectum
43	chr12:75947600-75947800	Enhancers	Fetal Stomach	stomach
44	chr12:75947600-75948000	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr12:75947600-75948200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:75947600-75948400	Enhancers	Right Ventricle	heart
47	chr12:75947600-75949400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:75947600-75954000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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