Variant report

Variant	rs12621278
Chromosome Location	chr2:173311553-173311554
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	chr2:173305610..173308515-chr2:173310023..173312671,2	MCF-7	breast:
2	chr2:173307073..173308885-chr2:173311042..173312605,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1001926	1.00[AFR][1000 genomes]
rs10187564	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10207640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10207654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10210544	0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10930559	1.00[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12052253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052385	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12053442	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12613307	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12615584	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12615596	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622724	1.00[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13387602	0.85[ASN][1000 genomes]
rs13410475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13414928	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes]
rs13421350	0.81[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs1574256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1574259	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860397	1.00[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16860416	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16860419	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16860426	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16860438	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16860478	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16860513	1.00[CEU][hapmap]
rs16860515	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16860634	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs2008518	1.00[AFR][1000 genomes]
rs2178476	1.00[AFR][1000 genomes]
rs2272496	1.00[AFR][1000 genomes]
rs2293645	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes]
rs2293647	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[AFR][1000 genomes]
rs2293648	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28485589	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3762618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4405725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55867175	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56882727	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56892098	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57244773	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs57404607	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs57587465	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs57878744	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59374567	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs59454075	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59970483	0.85[EUR][1000 genomes]
rs60096331	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6726739	0.83[CHD][hapmap];0.93[JPT][hapmap]
rs6730284	0.85[EUR][1000 genomes]
rs6741759	0.85[EUR][1000 genomes]
rs7564416	0.93[JPT][hapmap]
rs9636257	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Prostate cancer	19767753	GWAS catalog

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173305000-173316800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:173306800-173316400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:173307200-173318600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:173307400-173312800	Weak transcription	Fetal Kidney	kidney
5	chr2:173307400-173313600	Weak transcription	Placenta	Placenta
6	chr2:173307400-173322400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:173307600-173312400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:173307600-173312400	Weak transcription	Colonic Mucosa	Colon
9	chr2:173307600-173312600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:173307600-173312600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:173307600-173312600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:173307600-173313400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:173307600-173313600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:173307600-173313800	Weak transcription	Right Ventricle	heart
15	chr2:173307600-173314000	Enhancers	Duodenum Mucosa	Duodenum
16	chr2:173307600-173314600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:173307600-173314800	Weak transcription	Esophagus	oesophagus
18	chr2:173307600-173315600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:173307600-173321000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:173307800-173312400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:173308000-173312000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:173308000-173312600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:173308000-173313800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:173308200-173313400	Weak transcription	HepG2	liver
25	chr2:173308400-173312400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:173308400-173312600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr2:173309000-173312200	Weak transcription	A549	lung
28	chr2:173309000-173317000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:173309200-173315200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr2:173309400-173315600	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:173309600-173313000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:173309600-173313400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:173310000-173313200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:173310200-173311600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr2:173310200-173311800	Enhancers	Brain Germinal Matrix	brain
36	chr2:173310200-173312600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:173310400-173311600	Enhancers	Adipose Nuclei	Adipose
38	chr2:173310400-173311600	Enhancers	Stomach Mucosa	stomach
39	chr2:173310400-173311600	Enhancers	HUVEC	blood vessel
40	chr2:173310400-173311800	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr2:173310400-173312200	Enhancers	Primary T cells fromperipheralblood	blood
42	chr2:173310400-173312200	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr2:173310400-173313200	Enhancers	Primary T cells from cord blood	blood
44	chr2:173310400-173313200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:173310400-173314600	Enhancers	HMEC	breast
46	chr2:173310400-173318000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr2:173310600-173311600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:173310600-173311600	Enhancers	NH-A	brain
49	chr2:173310600-173311800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:173310600-173311800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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