Variant report

Variant	rs1331668
Chromosome Location	chr9:13143752-13143753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:13138755..13141262-chr9:13142656..13144698,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000107186	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10116304	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10116749	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10122431	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10125770	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10511577	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10733254	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10738323	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10738324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10738325	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10756454	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10756455	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10756456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10756457	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10756458	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10756459	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10756461	0.80[TSI][hapmap]
rs10809906	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10809907	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10809908	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10809912	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10809920	0.86[JPT][hapmap]
rs10960955	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10960958	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10960959	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12351444	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1330129	0.95[JPT][hapmap]
rs1331670	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1331672	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1331673	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1331674	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1331675	0.81[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs1360058	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1556421	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16930137	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1854414	0.93[EUR][1000 genomes]
rs1854907	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1854908	1.00[CEU][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1854909	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1929541	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1999393	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2225483	0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2274856	0.81[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2297003	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35068818	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3818595	0.87[CEU][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4237130	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58794982	0.88[ASN][1000 genomes]
rs6474753	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6474754	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6474755	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7024892	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7035244	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7037618	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7037704	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7039646	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7040347	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7859465	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7867993	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7871112	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7871575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9886797	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917331	chr9:12941193-13146852	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	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
3	nsv892582	chr9:13085379-13147764	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv528464	chr9:13137603-13147764	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	1 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	chr9:13103200-13163400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:13103200-13175600	Weak transcription	HepG2	liver
3	chr9:13105600-13144600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:13106000-13153400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:13121600-13225200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:13122600-13186400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr9:13135400-13223600	Weak transcription	Lung	lung
8	chr9:13136000-13192400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:13136200-13149400	Weak transcription	Fetal Heart	heart
10	chr9:13137400-13152800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:13138200-13161000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:13138800-13159800	Weak transcription	Aorta	Aorta
13	chr9:13138800-13191800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr9:13139000-13188200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:13139800-13147000	Weak transcription	Fetal Intestine Large	intestine
16	chr9:13139800-13147000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr9:13139800-13149600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:13139800-13174800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:13140200-13144400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:13140200-13144600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:13140200-13144600	Weak transcription	Ovary	ovary
22	chr9:13140200-13146800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr9:13140200-13146800	Weak transcription	Left Ventricle	heart
24	chr9:13140200-13147400	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:13140200-13149000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:13140200-13149200	Weak transcription	HSMMtube	muscle
27	chr9:13140200-13149600	Weak transcription	Psoas Muscle	Psoas
28	chr9:13140200-13152000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:13140200-13152200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr9:13140200-13153600	Weak transcription	Fetal Intestine Small	intestine
31	chr9:13140200-13157000	Weak transcription	Placenta	Placenta
32	chr9:13140200-13161200	Weak transcription	Fetal Stomach	stomach
33	chr9:13140200-13167800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr9:13140200-13174800	Weak transcription	Right Ventricle	heart
35	chr9:13141000-13146800	Enhancers	Fetal Lung	lung
36	chr9:13141000-13146800	Weak transcription	HSMM	muscle
37	chr9:13141000-13147000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:13141000-13181600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:13141000-13197800	Weak transcription	NHDF-Ad	bronchial
40	chr9:13141200-13144000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:13141200-13188200	Weak transcription	NHLF	lung
42	chr9:13141400-13146800	Weak transcription	NH-A	brain
43	chr9:13141600-13144200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr9:13141600-13147000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:13142000-13146600	Weak transcription	Liver	Liver
46	chr9:13142000-13146800	Weak transcription	Osteobl	bone
47	chr9:13142200-13145000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr9:13142200-13155800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr9:13143000-13143800	Enhancers	Fetal Brain Female	brain
50	chr9:13143000-13144000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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