Variant report

Variant	rs12622958
Chromosome Location	chr2:37880588-37880589
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:37878873..37880892-chr2:37884421..37886893,2	K562	blood:
2	chr2:37879997..37882658-chr2:37898189..37900305,3	MCF-7	breast:
3	chr2:37869759..37872018-chr2:37878989..37880854,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163171	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1013291	0.84[ASN][1000 genomes]
rs1013292	0.82[ASN][1000 genomes]
rs10694	0.83[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs11124594	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11124595	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11883958	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13387842	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13392288	0.84[ASN][1000 genomes]
rs13406302	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13417957	0.80[ASN][1000 genomes]
rs1468663	0.84[ASN][1000 genomes]
rs1468664	0.83[ASN][1000 genomes]
rs17021174	0.85[ASN][1000 genomes]
rs2041508	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2072419	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2079998	0.84[ASN][1000 genomes]
rs2098198	0.84[ASN][1000 genomes]
rs2109821	0.84[ASN][1000 genomes]
rs2109822	0.84[ASN][1000 genomes]
rs2159726	0.84[ASN][1000 genomes]
rs2191841	0.84[ASN][1000 genomes]
rs2373290	0.84[ASN][1000 genomes]
rs3731852	0.86[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs3731854	0.86[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4372883	0.84[ASN][1000 genomes]
rs4594425	0.84[ASN][1000 genomes]
rs4670210	0.90[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4670211	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4670748	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56809883	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6544095	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67084656	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6709067	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6709621	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6711909	0.83[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6722589	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6740127	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6752119	0.83[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6752220	0.86[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6752762	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6759224	0.90[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7607934	0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7735	0.83[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs9742	0.86[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]

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	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv535645	chr2:37853282-37972640	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv535646	chr2:37853282-38014428	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873880	chr2:37868214-37926046	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv535647	chr2:37874563-38014428	Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12622958	CDC42EP3	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37853600-37897400	Weak transcription	Small Intestine	intestine
2	chr2:37866800-37881000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:37867000-37880600	Genic enhancers	Muscle Satellite Cultured Cells	--
4	chr2:37871400-37880600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:37872000-37892400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr2:37872200-37881800	Weak transcription	Fetal Kidney	kidney
7	chr2:37872400-37880800	Weak transcription	Fetal Brain Male	brain
8	chr2:37873000-37881400	Enhancers	Right Atrium	heart
9	chr2:37873600-37881000	Weak transcription	Ovary	ovary
10	chr2:37873800-37889000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr2:37874200-37881600	Genic enhancers	NHLF	lung
12	chr2:37874400-37881600	Enhancers	Psoas Muscle	Psoas
13	chr2:37874400-37883200	Enhancers	Adipose Nuclei	Adipose
14	chr2:37874600-37884000	Enhancers	Fetal Muscle Leg	muscle
15	chr2:37874600-37893000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:37874800-37882000	Enhancers	Left Ventricle	heart
17	chr2:37875200-37881800	Enhancers	Spleen	Spleen
18	chr2:37875200-37882200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:37875400-37881200	Enhancers	Primary B cells from peripheral blood	blood
20	chr2:37875400-37883400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:37875600-37881000	Weak transcription	Fetal Brain Female	brain
22	chr2:37875600-37881200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:37875800-37881000	Weak transcription	Brain Germinal Matrix	brain
24	chr2:37875800-37881600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:37875800-37882000	Enhancers	Right Ventricle	heart
26	chr2:37875800-37883800	Genic enhancers	NHDF-Ad	bronchial
27	chr2:37875800-37884400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:37875800-37891800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr2:37875800-37893600	Weak transcription	Fetal Intestine Large	intestine
30	chr2:37875800-37896400	Weak transcription	Fetal Intestine Small	intestine
31	chr2:37876000-37880600	Weak transcription	Brain Angular Gyrus	brain
32	chr2:37876000-37881000	Weak transcription	Fetal Lung	lung
33	chr2:37876000-37881000	Genic enhancers	HSMM	muscle
34	chr2:37876000-37881200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:37876000-37882800	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr2:37876200-37880800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr2:37876200-37881000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr2:37876200-37881000	Weak transcription	Thymus	Thymus
39	chr2:37876200-37881200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:37876200-37881400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:37876200-37882600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:37876200-37884400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:37877000-37881000	Genic enhancers	HSMMtube	muscle
44	chr2:37877200-37882600	Enhancers	Colon Smooth Muscle	Colon
45	chr2:37877400-37883200	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr2:37877600-37880600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:37878000-37881000	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr2:37878000-37881800	Genic enhancers	Primary T cells fromperipheralblood	blood
49	chr2:37878000-37886200	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr2:37878200-37881000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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