Variant report

Variant	rs16859849
Chromosome Location	chr3:112339475-112339476
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	chr3:112338141..112343361-chr3:112351475..112354709,4	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10511317	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs1072896	1.00[AFR][1000 genomes]
rs11919639	1.00[CEU][hapmap]
rs12630906	1.00[AFR][1000 genomes]
rs12634199	1.00[AFR][1000 genomes]
rs12637057	1.00[AFR][1000 genomes]
rs12637953	1.00[AFR][1000 genomes]
rs13059364	1.00[AFR][1000 genomes]
rs13063173	1.00[AFR][1000 genomes]
rs13065703	1.00[CEU][hapmap]
rs13070342	1.00[CEU][hapmap]
rs13071492	1.00[CEU][hapmap]
rs13078401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13079599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13081265	1.00[AFR][1000 genomes]
rs13086960	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13094649	1.00[CEU][hapmap]
rs13095000	1.00[CEU][hapmap]
rs13096943	1.00[AFR][1000 genomes]
rs16845068	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16845073	1.00[AFR][1000 genomes]
rs16859661	1.00[CEU][hapmap]
rs16859674	1.00[CEU][hapmap]
rs16859727	1.00[CEU][hapmap]
rs16859758	1.00[AFR][1000 genomes]
rs16859890	1.00[AFR][1000 genomes]
rs16859897	1.00[AFR][1000 genomes]
rs16859930	1.00[AFR][1000 genomes]
rs16859961	1.00[AFR][1000 genomes]
rs28364588	1.00[AFR][1000 genomes]
rs28364589	1.00[AFR][1000 genomes]
rs28365853	1.00[CEU][hapmap]
rs34080815	1.00[AFR][1000 genomes]
rs34541731	1.00[AFR][1000 genomes]
rs34694961	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34829517	1.00[AFR][1000 genomes]
rs34889961	1.00[AFR][1000 genomes]
rs34949685	1.00[AFR][1000 genomes]
rs34962178	1.00[AFR][1000 genomes]
rs35263368	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35526995	1.00[AFR][1000 genomes]
rs35931975	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs36045008	1.00[AFR][1000 genomes]
rs36153507	1.00[AFR][1000 genomes]
rs3736269	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs3736270	1.00[CEU][hapmap]
rs3736271	1.00[CEU][hapmap]
rs3773701	1.00[AFR][1000 genomes]
rs3773704	1.00[AFR][1000 genomes]
rs3773706	1.00[CEU][hapmap]
rs3821684	1.00[CEU][hapmap]
rs56952692	1.00[AFR][1000 genomes]
rs57224143	1.00[AFR][1000 genomes]
rs59191788	1.00[AFR][1000 genomes]
rs59650289	1.00[AFR][1000 genomes]
rs60340975	1.00[AFR][1000 genomes]
rs60646325	1.00[AFR][1000 genomes]
rs60733172	1.00[AFR][1000 genomes]
rs66546764	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66791711	1.00[AFR][1000 genomes]
rs67021100	1.00[AFR][1000 genomes]
rs71317506	1.00[AFR][1000 genomes]
rs71317507	1.00[AFR][1000 genomes]
rs71317508	1.00[AFR][1000 genomes]
rs724125	1.00[CEU][hapmap]
rs73229350	1.00[AFR][1000 genomes]
rs73229353	1.00[AFR][1000 genomes]
rs958935	1.00[CEU][hapmap]
rs963541	1.00[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:112312600-112346200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:112312600-112347200	Weak transcription	Fetal Intestine Large	intestine
4	chr3:112316200-112342800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:112318000-112341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:112327800-112340600	Weak transcription	Fetal Kidney	kidney
7	chr3:112329600-112341800	Strong transcription	HSMM	muscle
8	chr3:112330400-112346800	Strong transcription	NHLF	lung
9	chr3:112331200-112351600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:112331400-112354800	Weak transcription	Psoas Muscle	Psoas
11	chr3:112335000-112340000	Weak transcription	Aorta	Aorta
12	chr3:112335200-112339800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:112335200-112340400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:112335200-112342200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:112335200-112345400	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:112336000-112342000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:112336200-112342000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:112336200-112347400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:112336200-112351600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:112336400-112341200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:112336400-112342000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:112336400-112346800	Weak transcription	Fetal Stomach	stomach
23	chr3:112336600-112351400	Weak transcription	Fetal Lung	lung
24	chr3:112336600-112355800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:112337000-112340000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:112337000-112346800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:112337600-112340000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:112337600-112340000	Weak transcription	Ovary	ovary
29	chr3:112337800-112340600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:112338000-112340000	Weak transcription	Adipose Nuclei	Adipose
31	chr3:112338000-112340200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:112338000-112349400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:112338400-112340000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:112338400-112340200	Weak transcription	HSMMtube	muscle
35	chr3:112338400-112346200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:112338600-112341200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:112338600-112341800	Weak transcription	K562	blood
38	chr3:112338600-112342000	Strong transcription	NH-A	brain
39	chr3:112338600-112342200	Weak transcription	HUVEC	blood vessel
40	chr3:112338800-112340000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:112338800-112340000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:112338800-112340200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:112338800-112340800	Weak transcription	NHDF-Ad	bronchial
44	chr3:112338800-112341800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:112338800-112341800	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:112338800-112343600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:112339000-112340000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:112339000-112340000	Weak transcription	A549	lung
49	chr3:112339000-112340400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr3:112339200-112339800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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