Variant report

Variant	rs16831246
Chromosome Location	chr2:153366129-153366130
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	chr2:153364136..153366729-chr2:153467251..153469526,2	MCF-7	breast:
2	chr2:153365869..153368986-chr2:153378102..153382040,3	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10931146	0.81[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12105467	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989726	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12992900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13033468	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16831135	0.92[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16831229	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16831247	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16831263	0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs2881338	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34027587	0.86[EUR][1000 genomes]
rs34520795	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35455499	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4664108	0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs4664111	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4664584	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4664588	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60280470	0.83[EUR][1000 genomes]
rs67374211	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739557	1.00[CEU][hapmap]
rs71417228	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7582905	0.84[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2754362	chr2:153297577-153366129	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153348800-153370200	Weak transcription	Aorta	Aorta
2	chr2:153357400-153375200	Weak transcription	Right Atrium	heart
3	chr2:153361000-153398600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:153361600-153369800	Weak transcription	NHDF-Ad	bronchial
5	chr2:153362400-153379400	Weak transcription	Fetal Brain Male	brain
6	chr2:153363800-153369800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:153364200-153369600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:153364200-153369800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:153365000-153377600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:153365200-153366800	Weak transcription	NHEK	skin
11	chr2:153365200-153369000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:153365200-153369800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:153365400-153368200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:153365400-153369400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:153365400-153369800	Weak transcription	HSMM	muscle
16	chr2:153365400-153370400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:153365400-153377200	Weak transcription	Small Intestine	intestine
18	chr2:153365600-153367200	Weak transcription	Fetal Lung	lung
19	chr2:153365600-153367200	Weak transcription	Pancreas	Pancrea
20	chr2:153365600-153368200	Weak transcription	Psoas Muscle	Psoas
21	chr2:153365600-153368400	Weak transcription	Brain Substantia Nigra	brain
22	chr2:153365600-153368600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:153365600-153368800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:153365600-153369200	Weak transcription	Brain Angular Gyrus	brain
25	chr2:153365600-153369200	Weak transcription	Hela-S3	cervix
26	chr2:153365600-153369400	Weak transcription	HMEC	breast
27	chr2:153365600-153369400	Weak transcription	HUVEC	blood vessel
28	chr2:153365600-153369400	Weak transcription	Osteobl	bone
29	chr2:153365600-153369600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:153365600-153369800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:153365600-153370200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:153365600-153370200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:153365600-153370200	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:153365600-153375200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:153365600-153386000	Weak transcription	Fetal Stomach	stomach
36	chr2:153365800-153367000	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:153365800-153368200	Weak transcription	A549	lung
38	chr2:153365800-153368600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:153365800-153369600	Weak transcription	Brain Anterior Caudate	brain
40	chr2:153365800-153369600	Weak transcription	NH-A	brain
41	chr2:153365800-153369800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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