Variant report

Variant	rs9341539
Chromosome Location	chr6:76592530-76592531
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12154202	0.81[AFR][1000 genomes]
rs1280049	0.92[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1280050	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1280051	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1280052	0.92[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1280053	0.92[CEU][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1280054	0.92[CEU][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1280055	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1280056	0.92[CEU][hapmap];0.80[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1280057	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1280058	0.92[CEU][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13202519	1.00[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13216921	0.82[LWK][hapmap]
rs1322549	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1335043	1.00[CEU][hapmap];0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34090650	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3778007	1.00[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3798426	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3798427	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3798429	0.92[CEU][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4476795	1.00[CEU][hapmap];0.80[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6914716	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6924528	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6932992	1.00[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7742567	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7767675	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs910679	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9341540	0.81[AFR][1000 genomes]
rs9343325	1.00[CEU][hapmap];0.80[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9343327	0.96[CEU][hapmap];0.80[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9359141	0.96[CEU][hapmap];0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9359147	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9360954	0.92[CEU][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9766905	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019328	chr6:76154751-76604197	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv538314	chr6:76154751-76604197	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1021090	chr6:76306100-76759397	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv538318	chr6:76306100-76759397	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1032961	chr6:76343575-76788852	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv932201	chr6:76365548-77219650	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1028340	chr6:76410921-76960225	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv538319	chr6:76410921-76960225	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76543000-76615000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:76544400-76603800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:76562400-76599800	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:76563400-76602800	Weak transcription	Small Intestine	intestine
5	chr6:76566200-76604600	Weak transcription	Right Ventricle	heart
6	chr6:76567000-76604400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:76567600-76598600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:76567600-76604200	Weak transcription	NHLF	lung
9	chr6:76573000-76597800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:76573000-76624000	Weak transcription	Placenta	Placenta
11	chr6:76573200-76604200	Weak transcription	Colonic Mucosa	Colon
12	chr6:76573400-76592800	Weak transcription	Stomach Mucosa	stomach
13	chr6:76573600-76606200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:76573800-76607200	Weak transcription	Gastric	stomach
15	chr6:76573800-76608400	Weak transcription	Esophagus	oesophagus
16	chr6:76574400-76632600	Weak transcription	Spleen	Spleen
17	chr6:76576000-76604000	Weak transcription	Fetal Brain Female	brain
18	chr6:76577200-76624600	Weak transcription	Fetal Kidney	kidney
19	chr6:76577400-76594000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:76581000-76594800	Strong transcription	Fetal Intestine Large	intestine
21	chr6:76582000-76593200	Weak transcription	Fetal Brain Male	brain
22	chr6:76583400-76606200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:76583800-76603000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:76583800-76624600	Weak transcription	Pancreas	Pancrea
25	chr6:76584000-76605600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:76584200-76608400	Weak transcription	Aorta	Aorta
27	chr6:76584200-76629400	Weak transcription	Ovary	ovary
28	chr6:76584400-76593000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:76584400-76593200	Weak transcription	HSMMtube	muscle
30	chr6:76584400-76594400	Weak transcription	HUVEC	blood vessel
31	chr6:76584400-76596400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:76584400-76623800	Weak transcription	Lung	lung
33	chr6:76584600-76596600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:76584800-76596400	Weak transcription	Brain Angular Gyrus	brain
35	chr6:76584800-76598200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:76584800-76615200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr6:76584800-76644600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:76585000-76608200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:76585800-76608000	Weak transcription	NH-A	brain
40	chr6:76585800-76624000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:76585800-76624400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:76585800-76626800	Weak transcription	Left Ventricle	heart
43	chr6:76585800-76644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:76586000-76597600	Weak transcription	Fetal Stomach	stomach
45	chr6:76586000-76627600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:76586200-76594000	Weak transcription	Liver	Liver
47	chr6:76586200-76624400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr6:76586400-76607800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:76587600-76623800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:76589000-76603200	Weak transcription	Brain Cingulate Gyrus	brain

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