Variant report

Variant	rs1535501
Chromosome Location	chr6:76598904-76598905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10806048	0.88[EUR][1000 genomes]
rs10943292	0.96[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs11970551	0.88[EUR][1000 genomes]
rs12209903	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12526227	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12662659	0.88[EUR][1000 genomes]
rs1322551	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1358954	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1407510	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2004170	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2181245	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2181246	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2273859	0.96[CEU][hapmap];0.86[GIH][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs2312940	0.82[ASN][1000 genomes]
rs2647404	0.85[JPT][hapmap]
rs2748959	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2748964	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2842538	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2842540	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2842542	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2842544	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2842546	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2842549	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap]
rs3798447	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3798448	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6934542	0.88[EUR][1000 genomes]
rs699186	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs720862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs720863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72890648	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9294005	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9443195	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9447579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	nsv933382	chr6:76596109-76599626	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
10	nsv934052	chr6:76596109-76599823	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1535501	SENP6	cis	parietal	SCAN
rs1535501	MYO6	cis	cerebellum	SCAN
rs1535501	TMEM30A	cis	parietal	SCAN

Chromatin state (count:70 , 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	chr6:76567600-76604200	Weak transcription	NHLF	lung
8	chr6:76573000-76624000	Weak transcription	Placenta	Placenta
9	chr6:76573200-76604200	Weak transcription	Colonic Mucosa	Colon
10	chr6:76573600-76606200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:76573800-76607200	Weak transcription	Gastric	stomach
12	chr6:76573800-76608400	Weak transcription	Esophagus	oesophagus
13	chr6:76574400-76632600	Weak transcription	Spleen	Spleen
14	chr6:76576000-76604000	Weak transcription	Fetal Brain Female	brain
15	chr6:76577200-76624600	Weak transcription	Fetal Kidney	kidney
16	chr6:76583400-76606200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:76583800-76603000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:76583800-76624600	Weak transcription	Pancreas	Pancrea
19	chr6:76584000-76605600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:76584200-76608400	Weak transcription	Aorta	Aorta
21	chr6:76584200-76629400	Weak transcription	Ovary	ovary
22	chr6:76584400-76623800	Weak transcription	Lung	lung
23	chr6:76584800-76615200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:76584800-76644600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:76585000-76608200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:76585800-76608000	Weak transcription	NH-A	brain
27	chr6:76585800-76624000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:76585800-76624400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:76585800-76626800	Weak transcription	Left Ventricle	heart
30	chr6:76585800-76644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:76586000-76627600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:76586200-76624400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr6:76586400-76607800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:76587600-76623800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:76589000-76603200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:76591600-76603200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:76592000-76606000	Weak transcription	Adipose Nuclei	Adipose
38	chr6:76592200-76605400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:76592600-76624400	Weak transcription	Osteobl	bone
40	chr6:76592800-76599800	Weak transcription	HMEC	breast
41	chr6:76592800-76600000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr6:76592800-76601800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:76592800-76606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:76592800-76631800	Weak transcription	NHEK	skin
45	chr6:76593000-76603600	Weak transcription	Brain Hippocampus Middle	brain
46	chr6:76593000-76603800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:76593200-76606000	Weak transcription	HSMM	muscle
48	chr6:76593200-76606200	Weak transcription	NHDF-Ad	bronchial
49	chr6:76594400-76599800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:76594400-76608400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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