Variant report

Variant	rs2594551
Chromosome Location	chr3:81790290-81790291
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:81789146..81795604-chr3:81809193..81811958,7	MCF-7	breast:
2	chr3:81789819..81797196-chr3:81807650..81813820,9	K562	blood:
3	chr3:81788513..81790945-chr3:81793476..81795825,2	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	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1155277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11711331	0.83[GIH][hapmap]
rs1375086	1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2372908	0.86[MEX][hapmap]
rs2594547	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]
rs2594549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2594553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2594558	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2594562	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2680245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2680246	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2680257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2680260	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2680264	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2680277	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2680280	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs2691093	0.96[CEU][hapmap];0.89[GIH][hapmap]
rs3107240	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772882	0.87[GIH][hapmap]
rs3772883	0.87[GIH][hapmap]
rs3772889	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772899	0.96[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap]
rs3772902	0.96[CEU][hapmap];0.91[GIH][hapmap];0.87[TSI][hapmap]
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	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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];0.98[TSI][hapmap];0.81[AMR][1000 genomes]
rs7620240	0.81[GIH][hapmap]
rs7648237	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9309876	0.80[AMR][1000 genomes]
rs9818090	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9846154	0.87[ASW][hapmap];0.86[MEX][hapmap]
rs9852545	0.85[AMR][1000 genomes]
rs9860805	0.96[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.82[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
rs2594551	GRIN1	trans	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:81727200-81792200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:81766600-81791200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:81773200-81792200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:81776000-81807400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:81779200-81791200	Weak transcription	Liver	Liver
6	chr3:81781000-81792200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr3:81781000-81809400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:81782200-81800400	Weak transcription	Primary B cells from cord blood	blood
9	chr3:81782400-81800200	Weak transcription	Left Ventricle	heart
10	chr3:81782800-81791200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:81782800-81796600	Weak transcription	Right Atrium	heart
12	chr3:81784600-81791000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:81784800-81792800	Weak transcription	HepG2	liver
14	chr3:81785200-81793000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:81785600-81793000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:81785800-81790600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:81785800-81791200	Weak transcription	HMEC	breast
18	chr3:81785800-81791200	Weak transcription	NHEK	skin
19	chr3:81785800-81791400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:81785800-81791600	Weak transcription	Psoas Muscle	Psoas
21	chr3:81786000-81791800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:81786200-81791200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:81788600-81792600	Strong transcription	Dnd41	blood
24	chr3:81789000-81792200	Weak transcription	Fetal Lung	lung
25	chr3:81789200-81794400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:81789600-81790600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr3:81789600-81790600	Enhancers	HSMM	muscle
28	chr3:81789600-81790800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:81789600-81790800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:81789600-81790800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:81789600-81790800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr3:81789600-81790800	Flanking Active TSS	HSMMtube	muscle
33	chr3:81789600-81791200	Enhancers	A549	lung
34	chr3:81789600-81791600	Enhancers	NHLF	lung
35	chr3:81789600-81791800	Enhancers	NHDF-Ad	bronchial
36	chr3:81789600-81791800	Enhancers	Osteobl	bone
37	chr3:81789600-81793600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:81789600-81794400	Enhancers	Fetal Heart	heart
39	chr3:81789600-81794600	Enhancers	Hela-S3	cervix
40	chr3:81789600-81794800	Enhancers	Adipose Nuclei	Adipose
41	chr3:81789800-81790400	Enhancers	Fetal Brain Male	brain
42	chr3:81789800-81791600	Enhancers	NH-A	brain
43	chr3:81790000-81790600	Weak transcription	Right Ventricle	heart
44	chr3:81790000-81790800	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr3:81790000-81791400	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr3:81790000-81791800	Enhancers	HUVEC	blood vessel
47	chr3:81790000-81793400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:81790200-81790400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:81790200-81790600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr3:81790200-81790600	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links