Variant report

Variant	rs2346201
Chromosome Location	chr2:153237974-153237975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153232621..153235253-chr2:153237551..153240252,2	K562	blood:
2	chr2:153233753..153235879-chr2:153237551..153240472,2	K562	blood:
3	chr2:153237750..153240255-chr2:153243184..153245369,2	K562	blood:
4	chr2:153231246..153233171-chr2:153235303..153238284,3	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10184210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931075	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931089	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11892662	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11898429	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12474369	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12614465	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16831066	0.81[JPT][hapmap]
rs2346202	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35547021	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3811575	0.81[JPT][hapmap]
rs3901192	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4371310	0.84[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs4664583	0.83[JPT][hapmap]
rs56322636	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57851180	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59348655	0.87[ASN][1000 genomes]
rs6434028	0.81[JPT][hapmap]
rs6721741	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6724305	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6736856	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7602505	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9677373	0.94[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9678076	0.88[ASN][1000 genomes]
rs9678127	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1005012	chr2:153206764-153273886	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153206800-153240800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:153207600-153246400	Weak transcription	Fetal Intestine Small	intestine
3	chr2:153224800-153246000	Weak transcription	Fetal Stomach	stomach
4	chr2:153226200-153249400	Weak transcription	Right Ventricle	heart
5	chr2:153226200-153251800	Weak transcription	HSMMtube	muscle
6	chr2:153226800-153240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:153227000-153242000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:153227800-153239400	Weak transcription	NHDF-Ad	bronchial
9	chr2:153229200-153252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:153232600-153239400	Enhancers	Brain Substantia Nigra	brain
11	chr2:153233000-153238400	Enhancers	Brain Angular Gyrus	brain
12	chr2:153233200-153240000	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:153233200-153242200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:153233400-153249000	Weak transcription	Gastric	stomach
15	chr2:153233600-153239000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:153233600-153246200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:153233800-153245600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:153233800-153255400	Weak transcription	NHEK	skin
19	chr2:153234600-153238400	Weak transcription	Lung	lung
20	chr2:153234600-153239600	Enhancers	Brain Hippocampus Middle	brain
21	chr2:153235000-153238200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:153235000-153239200	Enhancers	Brain Anterior Caudate	brain
23	chr2:153235000-153239600	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:153235200-153238400	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr2:153235400-153243200	Weak transcription	Stomach Mucosa	stomach
26	chr2:153236600-153238000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr2:153236600-153239000	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr2:153236800-153239000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:153236800-153239800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr2:153237000-153238000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:153237000-153238000	Enhancers	Right Atrium	heart
32	chr2:153237000-153238000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr2:153237000-153238400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:153237000-153238400	Enhancers	Adipose Nuclei	Adipose
35	chr2:153237000-153238600	Enhancers	Left Ventricle	heart
36	chr2:153237000-153238600	Enhancers	Ovary	ovary
37	chr2:153237000-153239200	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr2:153237000-153239800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:153237200-153238000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:153237200-153239200	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr2:153237400-153238400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:153237400-153239400	Weak transcription	NHLF	lung
43	chr2:153237400-153240200	Weak transcription	HepG2	liver
44	chr2:153237400-153240800	Weak transcription	Pancreas	Pancrea
45	chr2:153237400-153240800	Weak transcription	A549	lung
46	chr2:153237400-153246200	Weak transcription	Placenta	Placenta
47	chr2:153237400-153249000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:153237400-153255400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:153237400-153255400	Weak transcription	HMEC	breast
50	chr2:153237600-153238200	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links