Variant report

Variant	rs12477594
Chromosome Location	chr2:173325356-173325357
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	chr2:173320793..173322566-chr2:173325005..173326952,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10171775	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10175670	0.90[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs10195932	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10197251	0.91[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs10497381	0.91[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs10497385	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1076595	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10803874	0.82[MEX][hapmap]
rs12465295	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12465442	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12467358	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12469875	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.84[ASN][1000 genomes]
rs12469958	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12473999	0.82[ASN][1000 genomes]
rs12474168	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12474995	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12475916	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12476126	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12477247	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12478465	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12619242	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12622044	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12622687	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13383151	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13402061	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1344272	0.82[JPT][hapmap]
rs1574247	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16860377	0.91[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs16860497	0.93[MEX][hapmap]
rs16860543	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2178474	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2293646	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2293649	0.82[JPT][hapmap]
rs2357415	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34094408	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3749148	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3762619	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3792257	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3792260	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3934627	0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4281870	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4308101	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4480959	0.91[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs4619573	0.82[JPT][hapmap]
rs56084828	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57957394	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs58016698	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs58044442	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59020762	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59610589	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs60275829	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60446415	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6718477	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6755100	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7564591	0.82[JPT][hapmap]
rs7564654	0.82[JPT][hapmap]
rs7565216	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7582972	0.81[JPT][hapmap]
rs7591883	0.87[AMR][1000 genomes];0.84[ASN][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

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173317200-173325400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:173317600-173326000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:173317600-173326000	Weak transcription	Brain Substantia Nigra	brain
4	chr2:173318800-173326200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr2:173319200-173330600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:173319800-173326400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:173320000-173325400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:173320200-173326600	Enhancers	Duodenum Mucosa	Duodenum
9	chr2:173320600-173327200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:173320800-173325400	Enhancers	HMEC	breast
11	chr2:173320800-173326200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:173321000-173325400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:173321000-173326000	Weak transcription	HepG2	liver
14	chr2:173321000-173326400	Weak transcription	Right Ventricle	heart
15	chr2:173321000-173328000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:173321200-173325400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr2:173321200-173325800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:173321200-173325800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:173321200-173326200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:173321200-173326200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:173321200-173326400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:173321200-173327400	Weak transcription	Small Intestine	intestine
23	chr2:173321400-173325400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr2:173321400-173325400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:173321400-173325600	Weak transcription	Adipose Nuclei	Adipose
26	chr2:173321400-173325800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:173321400-173325800	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:173321400-173326000	Weak transcription	Fetal Intestine Large	intestine
29	chr2:173321400-173326200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:173321400-173326200	Weak transcription	Gastric	stomach
31	chr2:173321400-173326200	Weak transcription	Lung	lung
32	chr2:173321400-173326200	Weak transcription	Right Atrium	heart
33	chr2:173321400-173326400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:173321400-173327000	Weak transcription	Placenta	Placenta
35	chr2:173321400-173356000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:173322000-173325600	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr2:173322200-173326200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr2:173322200-173326400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr2:173322400-173326600	Enhancers	Primary T cells fromperipheralblood	blood
40	chr2:173322600-173325800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:173322600-173326800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr2:173322600-173327000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:173322600-173327200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr2:173322600-173327400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:173322800-173326200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:173322800-173326200	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr2:173323200-173326200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:173323200-173328400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:173323400-173325600	Weak transcription	HSMM	muscle
50	chr2:173323400-173326200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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