Variant report

Variant	rs3106796
Chromosome Location	chr2:189849773-189849774
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:189378368..189379278-chr2:189848607..189850003,3	MCF-7	breast:
2	chr2:189465598..189467415-chr2:189847399..189849894,2	MCF-7	breast:
3	chr2:189849262..189851265-chr2:189851542..189854419,2	MCF-7	breast:
4	chr2:189843846..189845833-chr2:189848371..189850816,2	K562	blood:
5	chr2:189840465..189844920-chr2:189846827..189849857,3	MCF-7	breast:
6	chr2:189468604..189471181-chr2:189847592..189850287,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221502	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12693525	0.86[CHD][hapmap]
rs2056156	1.00[ASW][hapmap];0.80[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2203601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3106798	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3106801	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3134646	0.86[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[YRI][hapmap]
rs3134656	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459992	chr2:189796272-189855943	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv584057	chr2:189796272-189855943	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875609	chr2:189796272-189862097	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv875610	chr2:189796272-189904674	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv584058	chr2:189799499-189855943	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
6	esv1791841	chr2:189811074-189864582	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv584059	chr2:189841052-189868381	Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv875612	chr2:189841052-189878769	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv584060	chr2:189844000-189876138	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv584061	chr2:189844000-189878769	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3106796	MSTN	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189839400-189858000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:189841400-189864000	Weak transcription	Left Ventricle	heart
3	chr2:189841800-189875200	Weak transcription	Colonic Mucosa	Colon
4	chr2:189842400-189866600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:189843400-189861800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:189843600-189874200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:189844400-189866200	Weak transcription	Psoas Muscle	Psoas
8	chr2:189844600-189859000	Weak transcription	Fetal Intestine Small	intestine
9	chr2:189844800-189850800	Enhancers	Rectal Smooth Muscle	rectum
10	chr2:189844800-189851400	Weak transcription	Fetal Kidney	kidney
11	chr2:189844800-189857200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:189847600-189850000	Enhancers	HSMMtube	muscle
13	chr2:189847600-189879200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:189847800-189858600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:189848200-189858000	Weak transcription	Aorta	Aorta
16	chr2:189848400-189851800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:189848400-189851800	Genic enhancers	Osteobl	bone
18	chr2:189848800-189850000	Enhancers	NH-A	brain
19	chr2:189848800-189851800	Genic enhancers	HSMM	muscle
20	chr2:189849000-189850000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:189849000-189850200	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:189849200-189849800	Genic enhancers	Fetal Lung	lung
23	chr2:189849200-189850200	Genic enhancers	NHLF	lung
24	chr2:189849200-189851000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:189849200-189852000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:189849400-189849800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr2:189849400-189849800	ZNF genes & repeats	Fetal Intestine Large	intestine
28	chr2:189849400-189849800	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
29	chr2:189849400-189849800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
30	chr2:189849400-189849800	Enhancers	Ovary	ovary
31	chr2:189849400-189849800	Genic enhancers	Rectal Mucosa Donor 29	rectum
32	chr2:189849400-189849800	Enhancers	A549	lung
33	chr2:189849400-189850000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:189849400-189852000	Genic enhancers	Adipose Nuclei	Adipose
35	chr2:189849400-189852200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:189849400-189877600	Strong transcription	Placenta	Placenta
37	chr2:189849600-189849800	Genic enhancers	Fetal Stomach	stomach
38	chr2:189849600-189850000	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
39	chr2:189849600-189850400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:189849600-189850600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:189849600-189851800	Genic enhancers	Colon Smooth Muscle	Colon
42	chr2:189849600-189876200	Strong transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links