Variant report

Variant	rs1331675
Chromosome Location	chr9:13177389-13177390
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	chr9:13176891..13178800-chr9:13180241..13181807,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10116304	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10116749	0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[ASN][1000 genomes]
rs10120857	0.86[ASN][1000 genomes]
rs10122431	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs10125770	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10511577	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs10733254	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10738323	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10738324	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs10738325	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10756454	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs10756455	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10756456	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs10756457	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs10756458	0.90[ASN][1000 genomes]
rs10756459	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10756460	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10756461	0.89[ASW][hapmap];0.88[CEU][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10809906	0.91[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs10809907	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10809912	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10809913	0.94[ASN][1000 genomes]
rs10809920	0.86[JPT][hapmap]
rs10960955	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs10960958	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10960959	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12351444	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1330129	0.95[JPT][hapmap]
rs1331668	0.81[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs1331670	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs1331672	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1331673	0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1331674	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1360058	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1556421	0.96[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16930137	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1854907	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1854908	1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs1854909	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1929541	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs1999393	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1999395	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2225483	0.83[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2274856	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297003	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs3780576	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3780577	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3818595	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs4237130	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs4741291	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58794982	0.80[ASN][1000 genomes]
rs6474753	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6474754	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.88[ASN][1000 genomes]
rs6474755	0.90[ASN][1000 genomes]
rs7024892	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs7035244	0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs7037618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7037704	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7039646	0.82[ASN][1000 genomes]
rs7040347	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72706366	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7859465	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7863888	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7867993	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs7871575	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9886797	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]

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	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv892583	chr9:13166139-13350478	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13121600-13225200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:13122600-13186400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:13135400-13223600	Weak transcription	Lung	lung
4	chr9:13136000-13192400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr9:13138800-13191800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr9:13139000-13188200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:13141000-13181600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:13141000-13197800	Weak transcription	NHDF-Ad	bronchial
9	chr9:13141200-13188200	Weak transcription	NHLF	lung
10	chr9:13143600-13202200	Weak transcription	Pancreas	Pancrea
11	chr9:13145400-13203200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:13145400-13228600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:13146600-13202400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:13147000-13178000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:13150000-13193200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:13150400-13180800	Weak transcription	A549	lung
17	chr9:13153200-13194800	Weak transcription	Fetal Kidney	kidney
18	chr9:13156800-13201400	Weak transcription	Psoas Muscle	Psoas
19	chr9:13158800-13188800	Weak transcription	Fetal Heart	heart
20	chr9:13160600-13183000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr9:13161600-13188200	Weak transcription	Fetal Stomach	stomach
22	chr9:13162200-13188200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:13163600-13202000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:13164200-13179400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:13164200-13188000	Weak transcription	Brain Hippocampus Middle	brain
26	chr9:13164200-13188800	Weak transcription	Brain Substantia Nigra	brain
27	chr9:13164200-13248600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr9:13164200-13258800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:13165800-13187400	Weak transcription	Brain Germinal Matrix	brain
30	chr9:13166000-13177400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:13166000-13181600	Weak transcription	HMEC	breast
32	chr9:13166400-13179200	Weak transcription	Fetal Brain Female	brain
33	chr9:13168000-13201800	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:13168400-13179000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:13168400-13179200	Weak transcription	HSMMtube	muscle
36	chr9:13168400-13181600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:13168400-13181600	Weak transcription	Brain Anterior Caudate	brain
38	chr9:13168400-13182600	Weak transcription	Fetal Lung	lung
39	chr9:13168400-13188200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr9:13168600-13181800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr9:13168600-13188200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr9:13170000-13188200	Weak transcription	Left Ventricle	heart
43	chr9:13171600-13181400	Weak transcription	NH-A	brain
44	chr9:13172000-13181000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:13172600-13181400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:13173000-13188800	Weak transcription	Spleen	Spleen
47	chr9:13174000-13181800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr9:13174200-13180200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr9:13174800-13177400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:13175000-13179000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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