Variant report

Variant	rs12815577
Chromosome Location	chr12:45656984-45656985
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	chr12:45608273..45611402-chr12:45650771..45657484,8	MCF-7	breast:
2	chr12:45655142..45658052-chr12:45658399..45661222,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177119	Chromatin interaction
ENSG00000134297	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1015626	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10437984	0.91[ASN][1000 genomes]
rs10459295	0.82[CEU][hapmap]
rs10748412	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785557	0.91[ASN][1000 genomes]
rs10785566	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap]
rs10880755	0.86[JPT][hapmap]
rs10880760	0.83[ASN][1000 genomes]
rs10880761	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10880762	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10880763	0.93[ASN][1000 genomes]
rs10880764	0.95[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10880765	0.82[CEU][hapmap]
rs10880766	0.82[CEU][hapmap]
rs11182905	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11182913	0.81[ASN][1000 genomes]
rs11182918	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11182936	0.93[ASN][1000 genomes]
rs11182938	0.93[ASN][1000 genomes]
rs11182939	0.93[ASN][1000 genomes]
rs11182944	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11182946	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11182947	0.95[AFR][1000 genomes]
rs11182949	0.95[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11182953	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11182954	0.82[CEU][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11182955	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11182957	0.82[CEU][hapmap]
rs11182961	0.82[CEU][hapmap]
rs11182965	0.82[CEU][hapmap]
rs11182981	0.82[CEU][hapmap]
rs11614082	0.82[CEU][hapmap]
rs12230322	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12231753	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12320168	0.87[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[ASN][1000 genomes]
rs12815334	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12815723	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12818421	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1399721	0.83[ASN][1000 genomes]
rs17095584	0.82[LWK][hapmap];1.00[AFR][1000 genomes]
rs1913692	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2012937	0.83[ASN][1000 genomes]
rs2052602	0.92[ASN][1000 genomes]
rs2052603	0.95[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2408184	0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[ASN][1000 genomes]
rs35660715	0.91[ASN][1000 genomes]
rs3759080	0.91[ASN][1000 genomes]
rs4768085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768598	0.83[ASN][1000 genomes]
rs4768601	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs57560057	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58444879	0.91[ASN][1000 genomes]
rs59569841	0.89[AFR][1000 genomes]
rs60840825	0.89[AFR][1000 genomes]
rs7138247	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs7138983	0.93[ASN][1000 genomes]
rs728590	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7304481	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307262	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7309615	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap]
rs7310046	0.83[ASN][1000 genomes]
rs73275009	0.97[AFR][1000 genomes]
rs73275012	0.97[AFR][1000 genomes]
rs73279680	0.85[AFR][1000 genomes]
rs73279683	0.89[AFR][1000 genomes]
rs73281425	0.89[AFR][1000 genomes]
rs73281431	0.84[AFR][1000 genomes]
rs73281433	0.83[AFR][1000 genomes]
rs73281436	0.87[AFR][1000 genomes]
rs73281453	0.89[AFR][1000 genomes]
rs73281454	0.89[AFR][1000 genomes]
rs73293382	1.00[AFR][1000 genomes]
rs7963038	0.90[ASN][1000 genomes]
rs7963057	0.90[ASN][1000 genomes]
rs7965430	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap]
rs7971900	0.86[JPT][hapmap]
rs9739519	0.91[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	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription 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	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45636200-45662400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:45648000-45657400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:45651200-45662000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:45651400-45662000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr12:45651400-45662400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:45651400-45675600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:45651600-45657200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:45651600-45662000	Weak transcription	Fetal Muscle Leg	muscle
9	chr12:45651600-45662400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:45651600-45667000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:45651600-45667400	Weak transcription	Brain Substantia Nigra	brain
12	chr12:45651600-45674000	Weak transcription	Primary B cells from cord blood	blood
13	chr12:45653800-45657400	Weak transcription	Small Intestine	intestine
14	chr12:45653800-45662000	Weak transcription	Esophagus	oesophagus
15	chr12:45654200-45657800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:45654200-45662000	Weak transcription	Right Ventricle	heart
17	chr12:45654200-45662000	Weak transcription	Spleen	Spleen
18	chr12:45654200-45662400	Weak transcription	Gastric	stomach
19	chr12:45654200-45666800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:45654400-45657000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:45654400-45657200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:45654400-45657200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:45654400-45657200	Weak transcription	Right Atrium	heart
24	chr12:45654400-45657200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:45654400-45657200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:45654400-45657200	Weak transcription	K562	blood
27	chr12:45654400-45657400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:45654400-45657400	Weak transcription	Fetal Kidney	kidney
29	chr12:45654400-45661800	Weak transcription	A549	lung
30	chr12:45654400-45662000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:45654400-45662000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:45654400-45662000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:45654400-45662000	Weak transcription	Osteobl	bone
34	chr12:45654400-45662400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:45654400-45662400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:45654400-45662400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:45654400-45662400	Weak transcription	Fetal Stomach	stomach
38	chr12:45654400-45662400	Weak transcription	HSMM	muscle
39	chr12:45654400-45662400	Weak transcription	NH-A	brain
40	chr12:45654400-45662400	Weak transcription	NHLF	lung
41	chr12:45654400-45662600	Weak transcription	Stomach Mucosa	stomach
42	chr12:45654400-45666600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr12:45654400-45667600	Weak transcription	Primary T cells from cord blood	blood
44	chr12:45654400-45725600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:45654600-45657200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:45654600-45660800	Weak transcription	NHEK	skin
47	chr12:45654800-45657200	Weak transcription	Fetal Thymus	thymus
48	chr12:45654800-45661200	Weak transcription	HMEC	breast
49	chr12:45654800-45662000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:45655000-45659400	Weak transcription	Pancreas	Pancrea

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