Variant report

Variant	rs13425379
Chromosome Location	chr2:189844599-189844600
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189843846..189845833-chr2:189848371..189850816,2	K562	blood:
2	chr2:189460620..189463074-chr2:189843714..189846986,3	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10191859	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10201930	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10208311	1.00[CEU][hapmap]
rs10497695	0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10497696	1.00[EUR][1000 genomes]
rs11902058	0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12105286	0.83[ASN][1000 genomes]
rs12105340	0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12619321	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13306257	0.83[ASN][1000 genomes]
rs13306260	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13306267	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13306268	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13306269	0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16830965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16830969	1.00[CEU][hapmap]
rs16830983	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16830984	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16831014	1.00[CEU][hapmap]
rs2271679	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs28413125	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28736387	0.81[ASN][1000 genomes]
rs3736488	0.81[ASN][1000 genomes]
rs3765160	0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3765161	0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs3768659	0.94[ASN][1000 genomes]
rs41263781	1.00[EUR][1000 genomes]
rs41272837	1.00[EUR][1000 genomes]
rs61112771	1.00[EUR][1000 genomes]
rs6711327	1.00[EUR][1000 genomes]
rs6730236	1.00[CEU][hapmap]
rs6741242	1.00[EUR][1000 genomes]
rs6752549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73047634	1.00[EUR][1000 genomes]
rs7567045	1.00[EUR][1000 genomes]
rs7576108	0.81[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7600151	1.00[EUR][1000 genomes]
rs7607614	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs8224	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv3418829	chr2:189843907-189847705	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	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
12	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

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189837800-189844800	Active TSS	Stomach Smooth Muscle	stomach
2	chr2:189838000-189844600	Active TSS	Right Atrium	heart
3	chr2:189838000-189844800	Active TSS	Adipose Nuclei	Adipose
4	chr2:189838000-189844800	Active TSS	NHLF	lung
5	chr2:189838200-189844800	Active TSS	Fetal Stomach	stomach
6	chr2:189838200-189846000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:189838200-189849400	Active TSS	Fetal Muscle Leg	muscle
8	chr2:189838400-189844600	Active TSS	Fetal Kidney	kidney
9	chr2:189838400-189844600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr2:189838400-189844800	Active TSS	Fetal Muscle Trunk	muscle
11	chr2:189838400-189845000	Active TSS	HSMMtube	muscle
12	chr2:189838600-189844600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:189838600-189844600	Active TSS	Rectal Smooth Muscle	rectum
14	chr2:189838600-189844800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:189838600-189844800	Active TSS	Colon Smooth Muscle	Colon
16	chr2:189838600-189844800	Active TSS	Ovary	ovary
17	chr2:189839400-189858000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:189841400-189864000	Weak transcription	Left Ventricle	heart
19	chr2:189841800-189844800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr2:189841800-189875200	Weak transcription	Colonic Mucosa	Colon
21	chr2:189842200-189844600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:189842400-189866600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:189842800-189844800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:189843000-189849400	Weak transcription	Placenta	Placenta
25	chr2:189843200-189844600	Flanking Active TSS	A549	lung
26	chr2:189843200-189844800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:189843200-189844800	Active TSS	Aorta	Aorta
28	chr2:189843200-189845000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:189843400-189861800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:189843600-189844800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:189843600-189845000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:189843600-189847200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr2:189843600-189874200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:189844000-189844600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:189844000-189844800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:189844000-189844800	Enhancers	HUVEC	blood vessel
37	chr2:189844000-189844800	Flanking Active TSS	Osteobl	bone
38	chr2:189844200-189844600	Active TSS	Fetal Intestine Small	intestine
39	chr2:189844200-189844600	Enhancers	Fetal Lung	lung
40	chr2:189844200-189844800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
41	chr2:189844400-189844800	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr2:189844400-189844800	Active TSS	HSMM	muscle
43	chr2:189844400-189844800	Enhancers	NH-A	brain
44	chr2:189844400-189849400	Weak transcription	Fetal Intestine Large	intestine
45	chr2:189844400-189866200	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links