Variant report

Variant	rs11898429
Chromosome Location	chr2:153237374-153237375
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: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10184210	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10931075	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10931089	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11885624	0.86[ASW][hapmap];0.84[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11892662	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12474369	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	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16831066	0.90[JPT][hapmap];0.82[YRI][hapmap]
rs2346201	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]
rs2346202	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35547021	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3811575	0.89[GIH][hapmap];0.90[JPT][hapmap]
rs3901192	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4371310	0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs4664583	0.89[JPT][hapmap]
rs56322636	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57851180	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59348655	0.85[ASN][1000 genomes]
rs6434028	0.89[GIH][hapmap];0.90[JPT][hapmap]
rs6721741	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6724305	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6736856	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7602505	0.82[ASN][1000 genomes]
rs9677373	0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9678076	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9678127	0.86[EUR][1000 genomes];0.92[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:59 , 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	chr2:153232000-153237400	Enhancers	HepG2	liver
11	chr2:153232600-153239400	Enhancers	Brain Substantia Nigra	brain
12	chr2:153233000-153238400	Enhancers	Brain Angular Gyrus	brain
13	chr2:153233200-153240000	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:153233200-153242200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:153233400-153237800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:153233400-153249000	Weak transcription	Gastric	stomach
17	chr2:153233600-153237800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:153233600-153239000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:153233600-153246200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:153233800-153237800	Weak transcription	Fetal Lung	lung
21	chr2:153233800-153245600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:153233800-153255400	Weak transcription	NHEK	skin
23	chr2:153234600-153238400	Weak transcription	Lung	lung
24	chr2:153234600-153239600	Enhancers	Brain Hippocampus Middle	brain
25	chr2:153235000-153238200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:153235000-153239200	Enhancers	Brain Anterior Caudate	brain
27	chr2:153235000-153239600	Enhancers	Brain Cingulate Gyrus	brain
28	chr2:153235200-153238400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr2:153235400-153243200	Weak transcription	Stomach Mucosa	stomach
30	chr2:153235800-153237800	Weak transcription	Psoas Muscle	Psoas
31	chr2:153236600-153237400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:153236600-153237400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:153236600-153237400	Enhancers	Placenta	Placenta
34	chr2:153236600-153238000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr2:153236600-153239000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:153236800-153239000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:153236800-153239800	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr2:153237000-153237400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr2:153237000-153237400	Enhancers	Pancreas	Pancrea
40	chr2:153237000-153237400	Enhancers	A549	lung
41	chr2:153237000-153237400	Enhancers	HMEC	breast
42	chr2:153237000-153237400	Enhancers	NHLF	lung
43	chr2:153237000-153237800	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr2:153237000-153238000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:153237000-153238000	Enhancers	Right Atrium	heart
46	chr2:153237000-153238000	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr2:153237000-153238400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:153237000-153238400	Enhancers	Adipose Nuclei	Adipose
49	chr2:153237000-153238600	Enhancers	Left Ventricle	heart
50	chr2:153237000-153238600	Enhancers	Ovary	ovary

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