Variant report

Variant	rs12474369
Chromosome Location	chr2:153236960-153236961
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	chr2:153231246..153233171-chr2:153235303..153238284,3	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10184210	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931075	0.95[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931089	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11892662	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11898429	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12614465	0.80[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2346201	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]
rs2346202	0.84[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35547021	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3901192	0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4371310	0.83[MEX][hapmap]
rs56322636	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57851180	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59348655	0.82[ASN][1000 genomes]
rs60292351	0.80[ASN][1000 genomes]
rs6721741	0.80[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6724305	0.80[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6736856	0.80[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7602505	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9677373	0.94[ASW][hapmap];0.84[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9678076	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9678127	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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:60 , 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	chr2:153209400-153237000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:153223400-153237000	Weak transcription	Right Atrium	heart
5	chr2:153224800-153246000	Weak transcription	Fetal Stomach	stomach
6	chr2:153226200-153237000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:153226200-153237000	Weak transcription	Aorta	Aorta
8	chr2:153226200-153237000	Weak transcription	Left Ventricle	heart
9	chr2:153226200-153249400	Weak transcription	Right Ventricle	heart
10	chr2:153226200-153251800	Weak transcription	HSMMtube	muscle
11	chr2:153226800-153237000	Weak transcription	NHLF	lung
12	chr2:153226800-153240000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:153227000-153237200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:153227000-153242000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:153227800-153239400	Weak transcription	NHDF-Ad	bronchial
16	chr2:153229200-153252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:153229600-153237000	Weak transcription	Fetal Kidney	kidney
18	chr2:153231400-153237000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:153232000-153237400	Enhancers	HepG2	liver
20	chr2:153232200-153237000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:153232600-153239400	Enhancers	Brain Substantia Nigra	brain
22	chr2:153233000-153238400	Enhancers	Brain Angular Gyrus	brain
23	chr2:153233200-153237000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:153233200-153237000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:153233200-153240000	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:153233200-153242200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:153233400-153237800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:153233400-153249000	Weak transcription	Gastric	stomach
29	chr2:153233600-153237000	Weak transcription	Pancreas	Pancrea
30	chr2:153233600-153237000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:153233600-153237800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr2:153233600-153239000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:153233600-153246200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:153233800-153237000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:153233800-153237000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:153233800-153237000	Weak transcription	HMEC	breast
37	chr2:153233800-153237800	Weak transcription	Fetal Lung	lung
38	chr2:153233800-153245600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:153233800-153255400	Weak transcription	NHEK	skin
40	chr2:153234600-153238400	Weak transcription	Lung	lung
41	chr2:153234600-153239600	Enhancers	Brain Hippocampus Middle	brain
42	chr2:153235000-153238200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:153235000-153239200	Enhancers	Brain Anterior Caudate	brain
44	chr2:153235000-153239600	Enhancers	Brain Cingulate Gyrus	brain
45	chr2:153235200-153238400	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr2:153235400-153237000	Weak transcription	Adipose Nuclei	Adipose
47	chr2:153235400-153237200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:153235400-153243200	Weak transcription	Stomach Mucosa	stomach
49	chr2:153235800-153237000	Weak transcription	Ovary	ovary
50	chr2:153235800-153237800	Weak transcription	Psoas Muscle	Psoas

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