Variant report

Variant	rs10947752
Chromosome Location	chr6:38553147-38553148
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	chr6:38535241..38537591-chr6:38552081..38553699,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10807196	0.82[EUR][1000 genomes]
rs10807198	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1321056	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1699001	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699002	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1699003	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699004	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1699005	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1699007	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699017	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1739621	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1739626	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1739628	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1739629	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1739630	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1739632	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1781708	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1781711	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1781712	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1852979	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2144328	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2252550	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2748165	0.81[EUR][1000 genomes]
rs2748172	0.89[EUR][1000 genomes]
rs2814883	0.82[EUR][1000 genomes]
rs2814885	0.82[EUR][1000 genomes]
rs2814889	0.83[EUR][1000 genomes]
rs2814894	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4392718	0.82[EUR][1000 genomes]
rs6458059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs910516	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9394521	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38519600-38554800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:38523000-38571600	Weak transcription	HSMMtube	muscle
3	chr6:38534400-38561600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:38535400-38554600	Weak transcription	Fetal Stomach	stomach
5	chr6:38535600-38555400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:38535600-38555800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:38535600-38556000	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:38535600-38556000	Weak transcription	NHLF	lung
9	chr6:38535600-38557600	Weak transcription	HSMM	muscle
10	chr6:38535800-38559800	Weak transcription	Fetal Lung	lung
11	chr6:38535800-38560200	Weak transcription	NH-A	brain
12	chr6:38535800-38564000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:38535800-38578200	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:38536200-38556000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:38536200-38559200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:38536400-38555800	Weak transcription	NHDF-Ad	bronchial
17	chr6:38536400-38560200	Weak transcription	Brain Angular Gyrus	brain
18	chr6:38536800-38566400	Weak transcription	Pancreas	Pancrea
19	chr6:38537000-38557200	Weak transcription	Thymus	Thymus
20	chr6:38538000-38566800	Weak transcription	Esophagus	oesophagus
21	chr6:38538200-38558600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:38538600-38561800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:38538600-38562000	Weak transcription	Brain Germinal Matrix	brain
24	chr6:38539800-38554800	Weak transcription	Lung	lung
25	chr6:38539800-38562800	Weak transcription	Fetal Thymus	thymus
26	chr6:38540400-38557800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:38540400-38560000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr6:38540400-38561600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:38540400-38567800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr6:38540400-38569200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:38540600-38559200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:38540600-38560000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:38541000-38565200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:38541400-38568600	Weak transcription	Spleen	Spleen
35	chr6:38541600-38567000	Weak transcription	Small Intestine	intestine
36	chr6:38541800-38555600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:38542000-38563400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:38542200-38558800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr6:38542800-38560200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:38543400-38560200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:38544400-38560000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr6:38544600-38558800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr6:38545000-38556000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:38545000-38561400	Weak transcription	Psoas Muscle	Psoas
45	chr6:38545200-38555600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr6:38545400-38555600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr6:38545400-38566000	Weak transcription	Colonic Mucosa	Colon
48	chr6:38546200-38563800	Weak transcription	Gastric	stomach
49	chr6:38546600-38559800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr6:38547200-38556600	Weak transcription	HMEC	breast

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