Variant report

Variant	rs2594547
Chromosome Location	chr3:81777680-81777681
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:81777151..81779498-chr3:81809848..81811917,2	MCF-7	breast:
2	chr3:81732567..81734878-chr3:81776708..81779542,2	K562	blood:
3	chr3:81776057..81778355-chr3:81808798..81811277,2	K562	blood:
4	chr3:81776433..81778191-chr3:81783098..81785714,2	K562	blood:
5	chr3:81771154..81772846-chr3:81777527..81780297,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114480	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11127737	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1155277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711331	0.83[GIH][hapmap]
rs1375086	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2372908	0.86[MEX][hapmap]
rs2594549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2594551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2594553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2594558	0.82[AMR][1000 genomes]
rs2594562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2680245	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs2680246	0.82[AMR][1000 genomes]
rs2680257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680260	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2680264	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2680277	0.95[CEU][hapmap];0.82[AMR][1000 genomes]
rs2680280	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs2691093	0.96[CEU][hapmap];0.89[GIH][hapmap]
rs3107240	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772882	0.87[GIH][hapmap]
rs3772883	0.87[GIH][hapmap]
rs3772889	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772899	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs3772902	0.96[CEU][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs3772914	0.86[MEX][hapmap]
rs3821548	0.83[GIH][hapmap]
rs3849570	0.83[GIH][hapmap]
rs3860595	0.91[GIH][hapmap]
rs4411908	0.87[GIH][hapmap]
rs6771266	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6785616	0.86[MEX][hapmap]
rs6800135	0.86[MEX][hapmap]
rs6803932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes]
rs7620240	0.81[GIH][hapmap]
rs7648237	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9309876	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9818090	0.96[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9846154	0.86[MEX][hapmap]
rs9852545	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9860805	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9869348	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012133	chr3:81499082-81817471	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv949545	chr3:81523898-81893929	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1009607	chr3:81651419-81825151	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv536604	chr3:81651419-81825151	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv834749	chr3:81655377-81818880	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv999992	chr3:81693662-82015969	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv536605	chr3:81693662-82015969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2594547	GRIN1	trans	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81727200-81792200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:81755800-81781000	Weak transcription	Primary B cells from cord blood	blood
3	chr3:81766600-81778400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:81766600-81791200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:81767400-81778400	Weak transcription	Left Ventricle	heart
6	chr3:81772400-81778400	Weak transcription	Aorta	Aorta
7	chr3:81773000-81778400	Weak transcription	Right Atrium	heart
8	chr3:81773000-81780800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:81773200-81778200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:81773200-81778400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:81773200-81792200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:81773400-81778400	Weak transcription	Right Ventricle	heart
13	chr3:81773400-81783600	Weak transcription	HepG2	liver
14	chr3:81774200-81780600	Weak transcription	Brain Substantia Nigra	brain
15	chr3:81774600-81784200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:81774800-81778600	Enhancers	HSMM	muscle
17	chr3:81775200-81778600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:81775400-81778800	Enhancers	NH-A	brain
19	chr3:81776000-81807400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:81776200-81778800	Weak transcription	Psoas Muscle	Psoas
21	chr3:81776200-81779200	Enhancers	Liver	Liver
22	chr3:81776200-81779200	Enhancers	Hela-S3	cervix
23	chr3:81776400-81789400	Weak transcription	HSMMtube	muscle
24	chr3:81776600-81778400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:81776600-81779000	Enhancers	HUVEC	blood vessel
26	chr3:81776600-81784800	Weak transcription	Adipose Nuclei	Adipose
27	chr3:81776800-81778400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:81776800-81778400	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr3:81777000-81778400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:81777000-81778600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:81777200-81779200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:81777400-81777800	Active TSS	A549	lung
33	chr3:81777600-81777800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:81777600-81777800	Enhancers	Colon Smooth Muscle	Colon
35	chr3:81777600-81778000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:81777600-81778000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:81777600-81778000	Flanking Active TSS	NHDF-Ad	bronchial
38	chr3:81777600-81778000	Flanking Active TSS	NHEK	skin
39	chr3:81777600-81778000	Active TSS	NHLF	lung
40	chr3:81777600-81778400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:81777600-81778400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr3:81777600-81778400	Enhancers	Dnd41	blood
43	chr3:81777600-81778400	Flanking Active TSS	Osteobl	bone
44	chr3:81777600-81779000	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr3:81777600-81779200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:81777600-81779600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links