Variant report

Variant	rs12309339
Chromosome Location	chr12:12660925-12660926
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12659166..12661033-chr12:12690816..12693581,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10845555	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845564	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845570	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845571	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10845573	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11054927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11054929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11054930	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11054931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11054938	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11054950	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11054961	1.00[MEX][hapmap];0.89[TSI][hapmap]
rs12314295	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12581531	0.89[MEX][hapmap]
rs2417188	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2909054	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2970802	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2970803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4421828	1.00[MEX][hapmap];0.89[TSI][hapmap]
rs4763287	0.96[AMR][1000 genomes]
rs7314806	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7961296	0.86[CHB][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes]
rs7978266	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs888201	0.81[CHB][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes]
rs888202	0.96[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv898811	chr12:12655443-12928295	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12630600-12661200	Weak transcription	NHEK	skin
2	chr12:12630800-12681000	Weak transcription	Colonic Mucosa	Colon
3	chr12:12634400-12685200	Weak transcription	Hela-S3	cervix
4	chr12:12639400-12679600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:12641600-12663600	Weak transcription	Lung	lung
6	chr12:12641600-12686200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:12647000-12661400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:12652800-12665000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:12653800-12669000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:12654000-12661200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:12654400-12667200	Weak transcription	Primary T cells from cord blood	blood
12	chr12:12656000-12666400	Weak transcription	Spleen	Spleen
13	chr12:12656800-12670800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:12658200-12661800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr12:12658200-12662800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr12:12658400-12662000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr12:12658400-12662600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr12:12658400-12662800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr12:12658800-12662200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr12:12658800-12662600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr12:12659000-12662800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:12659000-12667000	Weak transcription	Fetal Thymus	thymus
23	chr12:12659000-12669200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr12:12659200-12661200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:12659200-12661400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:12659400-12661400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:12659400-12663800	Enhancers	Brain Angular Gyrus	brain
28	chr12:12659400-12665200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:12659600-12661000	Enhancers	Fetal Muscle Leg	muscle
30	chr12:12659600-12662000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr12:12659600-12662800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:12659600-12663200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr12:12659600-12663800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:12659600-12664000	Enhancers	NHLF	lung
35	chr12:12659600-12664600	Enhancers	Osteobl	bone
36	chr12:12659600-12665800	Enhancers	Brain Cingulate Gyrus	brain
37	chr12:12659800-12661400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:12659800-12661400	Enhancers	GM12878-XiMat	blood
39	chr12:12659800-12662000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:12659800-12662000	Weak transcription	Stomach Mucosa	stomach
41	chr12:12659800-12662800	Weak transcription	A549	lung
42	chr12:12659800-12663000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr12:12659800-12664600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:12659800-12664600	Weak transcription	Thymus	Thymus
45	chr12:12659800-12665200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr12:12659800-12665600	Weak transcription	Fetal Intestine Small	intestine
47	chr12:12659800-12667800	Enhancers	Brain Hippocampus Middle	brain
48	chr12:12659800-12669000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:12659800-12669800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr12:12659800-12670800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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