Variant report

Variant	rs16865331
Chromosome Location	chr2:178392555-178392556
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	chr2:178390483..178393046-chr2:178411781..178414384,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10170546	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs10170667	0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10194648	0.82[ASN][1000 genomes]
rs10201153	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10497500	0.86[JPT][hapmap]
rs10497501	0.83[JPT][hapmap]
rs10497502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10497503	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10497508	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10930792	0.81[ASN][1000 genomes]
rs12469386	0.85[JPT][hapmap]
rs12612857	0.86[JPT][hapmap]
rs12615367	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12616093	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12618139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12990729	0.81[ASN][1000 genomes]
rs13000048	0.86[JPT][hapmap]
rs13004955	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1348848	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1348849	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1348850	0.95[JPT][hapmap]
rs1374437	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1405713	0.87[JPT][hapmap]
rs1453370	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1453373	0.81[JPT][hapmap]
rs1548067	0.86[JPT][hapmap]
rs16865203	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16865216	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16865229	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16865291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16865328	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1901825	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs1901826	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1979058	0.81[ASN][1000 genomes]
rs2034678	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2060929	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2084233	0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2121430	0.85[JPT][hapmap]
rs2166558	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2197611	0.82[ASN][1000 genomes]
rs2364853	0.91[ASN][1000 genomes]
rs2364854	0.86[JPT][hapmap]
rs3213945	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3769995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769996	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3769997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770002	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3813259	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs3902850	0.81[ASN][1000 genomes]
rs4243388	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs4528793	0.86[JPT][hapmap]
rs4893821	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4893822	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4893823	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs4893825	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4893935	0.85[JPT][hapmap]
rs4893936	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4893950	0.84[JPT][hapmap]
rs4893951	0.88[ASN][1000 genomes]
rs4893957	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs4893959	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4893961	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4893962	0.95[JPT][hapmap]
rs4893965	0.86[JPT][hapmap]
rs56942680	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57273542	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57295810	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57527255	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57541536	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57733896	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57948641	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58297927	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58483300	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59111239	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59421055	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59504156	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60642012	0.95[ASN][1000 genomes]
rs60670838	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60733259	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6433670	0.82[ASN][1000 genomes]
rs6433673	0.83[ASN][1000 genomes]
rs6710575	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6742951	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7587604	0.86[JPT][hapmap]
rs7591807	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7604673	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7606235	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7607450	0.82[ASN][1000 genomes]
rs8941	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs952746	0.86[JPT][hapmap]
rs9679607	0.81[ASN][1000 genomes]
rs9789582	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178296400-178397000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:178332000-178392800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:178332000-178393800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:178335000-178410600	Weak transcription	Thymus	Thymus
5	chr2:178338000-178403000	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:178339800-178394400	Weak transcription	Hela-S3	cervix
7	chr2:178348400-178402600	Weak transcription	NHDF-Ad	bronchial
8	chr2:178349800-178407800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:178350000-178407000	Weak transcription	Osteobl	bone
10	chr2:178356000-178405400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:178358600-178406000	Weak transcription	Ovary	ovary
12	chr2:178358600-178417000	Weak transcription	Aorta	Aorta
13	chr2:178358800-178396600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:178360600-178405400	Weak transcription	NH-A	brain
15	chr2:178362400-178395600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr2:178363000-178395600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr2:178364400-178416600	Weak transcription	Esophagus	oesophagus
18	chr2:178367800-178397200	Weak transcription	Psoas Muscle	Psoas
19	chr2:178371400-178399800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:178372600-178405400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:178372800-178399200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:178372800-178416600	Weak transcription	A549	lung
23	chr2:178374400-178394400	Strong transcription	HepG2	liver
24	chr2:178375200-178400800	Weak transcription	Lung	lung
25	chr2:178375400-178394400	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:178375600-178413800	Weak transcription	K562	blood
27	chr2:178376000-178397400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:178376200-178407800	Weak transcription	Left Ventricle	heart
29	chr2:178376200-178416600	Weak transcription	Pancreas	Pancrea
30	chr2:178376600-178407600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:178378400-178410000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:178379600-178407600	Weak transcription	Fetal Kidney	kidney
33	chr2:178379800-178406000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:178380400-178392600	Weak transcription	NHEK	skin
35	chr2:178384800-178393200	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:178384800-178395200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:178385000-178393600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:178385400-178392800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:178385400-178401000	Weak transcription	Fetal Intestine Small	intestine
40	chr2:178385400-178405000	Weak transcription	GM12878-XiMat	blood
41	chr2:178385800-178395200	Weak transcription	Right Ventricle	heart
42	chr2:178386000-178407400	Weak transcription	HSMMtube	muscle
43	chr2:178386600-178392800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr2:178386800-178405400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr2:178387000-178392800	Weak transcription	HUVEC	blood vessel
46	chr2:178387600-178402400	Weak transcription	Placenta	Placenta
47	chr2:178388600-178416600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:178388800-178405400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr2:178389000-178405200	Weak transcription	Fetal Intestine Large	intestine
50	chr2:178389000-178407800	Weak transcription	Fetal Muscle Trunk	muscle

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