Variant report

Variant	rs7611956
Chromosome Location	chr3:151151220-151151221
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10935848	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13088575	0.86[GIH][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs2087728	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2101647	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2172250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3975409	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680442	0.86[GIH][hapmap]
rs4680443	0.82[GIH][hapmap]
rs6440741	0.89[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs6440743	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792496	0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7621591	0.86[GIH][hapmap]
rs7652056	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs937119	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs937120	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs937127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840738	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9873499	0.83[ASN][1000 genomes]
rs9878370	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1000355	chr3:151108859-151243835	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv995048	chr3:151114074-151560019	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv877649	chr3:151147968-151236562	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7611956	GPR171	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151106000-151154600	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:151129400-151162800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:151133400-151154800	Weak transcription	Fetal Brain Male	brain
4	chr3:151133600-151151800	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:151135000-151152200	Weak transcription	Fetal Kidney	kidney
6	chr3:151140200-151152800	Weak transcription	Fetal Thymus	thymus
7	chr3:151140200-151154400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:151140200-151157000	Weak transcription	Dnd41	blood
9	chr3:151143000-151151600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:151143000-151151600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:151143200-151152600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:151143800-151154600	Weak transcription	Fetal Lung	lung
13	chr3:151144400-151152400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:151144400-151153200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:151144800-151155000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:151145000-151154600	Weak transcription	Ovary	ovary
17	chr3:151146400-151153400	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:151147200-151152400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:151147200-151157800	Weak transcription	Aorta	Aorta
20	chr3:151148400-151161400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:151148800-151162400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:151149000-151152600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:151149000-151153200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:151149200-151152200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:151149200-151152600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:151149400-151151400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:151149400-151152600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr3:151149600-151151600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:151149800-151151800	Enhancers	NHLF	lung
30	chr3:151150000-151152200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:151150000-151152600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:151150000-151156800	Weak transcription	Pancreas	Pancrea
33	chr3:151150200-151151400	Strong transcription	Primary hematopoietic stem cells	blood
34	chr3:151150200-151151800	Weak transcription	HMEC	breast
35	chr3:151150200-151152200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:151150200-151152200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:151150200-151152200	Enhancers	A549	lung
38	chr3:151150200-151152400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:151150200-151153400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:151150200-151153400	Enhancers	Osteobl	bone
41	chr3:151150400-151151400	Weak transcription	HSMM	muscle
42	chr3:151150400-151151800	Weak transcription	NHEK	skin
43	chr3:151150400-151157200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:151150400-151158200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:151151000-151153400	Enhancers	NH-A	brain
46	chr3:151151200-151152200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:151151200-151152400	Enhancers	NHDF-Ad	bronchial
48	chr3:151151200-151152800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:151151200-151158400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links