Variant report

Variant	rs3770888
Chromosome Location	chr2:36660989-36660990
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36587591..36589572-chr2:36660142..36662034,2	MCF-7	breast:
2	chr2:36581891..36584945-chr2:36659676..36663580,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260025	Chromatin interaction
ENSG00000150938	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11124512	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs11673762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1477048	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17018688	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs17018699	0.91[CHB][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs17018723	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs17018790	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs17018798	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2276673	0.97[EUR][1000 genomes]
rs34439217	0.96[EUR][1000 genomes]
rs3770883	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3770884	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770885	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3770886	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3770887	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3770891	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770897	0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3770899	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3770910	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs3770914	0.94[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs3770922	0.91[CHB][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs3770927	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs3821157	1.00[CEU][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3821164	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4670552	0.82[CHB][hapmap]
rs56036545	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57431226	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57785523	0.87[AFR][1000 genomes]
rs58185473	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62136162	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6729186	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7571902	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs876458	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833803	chr2:36589065-36745779	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36640200-36680000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:36644400-36665600	Weak transcription	Gastric	stomach
3	chr2:36649600-36662200	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr2:36650600-36676600	Weak transcription	Stomach Mucosa	stomach
5	chr2:36651600-36668400	Weak transcription	Fetal Intestine Small	intestine
6	chr2:36651600-36668400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:36651800-36668400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr2:36651800-36686800	Weak transcription	Colonic Mucosa	Colon
9	chr2:36652200-36668600	Weak transcription	Primary B cells from cord blood	blood
10	chr2:36653000-36667800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr2:36653400-36669400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:36655400-36662600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr2:36656800-36661000	Enhancers	Fetal Stomach	stomach
14	chr2:36657000-36665600	Genic enhancers	A549	lung
15	chr2:36657600-36661200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:36657600-36661600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr2:36658000-36668400	Weak transcription	Esophagus	oesophagus
18	chr2:36658200-36661000	Enhancers	Fetal Kidney	kidney
19	chr2:36658400-36665400	Enhancers	NHDF-Ad	bronchial
20	chr2:36658600-36661400	Enhancers	Fetal Lung	lung
21	chr2:36658800-36662200	Genic enhancers	HSMM	muscle
22	chr2:36659000-36661600	Enhancers	HUVEC	blood vessel
23	chr2:36659400-36661400	Enhancers	HepG2	liver
24	chr2:36659600-36661400	Enhancers	Fetal Heart	heart
25	chr2:36659600-36661800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:36659800-36661000	Enhancers	Left Ventricle	heart
27	chr2:36659800-36661200	Enhancers	NH-A	brain
28	chr2:36659800-36661600	Enhancers	Brain Substantia Nigra	brain
29	chr2:36660000-36661000	Enhancers	Brain Hippocampus Middle	brain
30	chr2:36660000-36661000	Enhancers	Fetal Brain Male	brain
31	chr2:36660000-36661000	Enhancers	Psoas Muscle	Psoas
32	chr2:36660000-36662000	Enhancers	Brain Anterior Caudate	brain
33	chr2:36660000-36662400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:36660200-36661000	Enhancers	Right Atrium	heart
35	chr2:36660200-36661000	Flanking Active TSS	Osteobl	bone
36	chr2:36660200-36661200	Enhancers	Brain Germinal Matrix	brain
37	chr2:36660200-36661400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:36660200-36661400	Enhancers	Brain Cingulate Gyrus	brain
39	chr2:36660200-36661600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:36660200-36661600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:36660200-36661800	Flanking Active TSS	NHEK	skin
42	chr2:36660200-36662200	Enhancers	HSMMtube	muscle
43	chr2:36660400-36661000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr2:36660400-36661000	Enhancers	Hela-S3	cervix
45	chr2:36660400-36661400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:36660400-36661600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:36660400-36662600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:36660400-36671800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr2:36660600-36661000	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr2:36660600-36661800	Enhancers	Rectal Smooth Muscle	rectum

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