Variant report

Variant	rs760783
Chromosome Location	chr6:35396004-35396005
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35226026..35228002-chr6:35394504..35397292,2	K562	blood:
2	chr6:35395055..35396641-chr6:35399730..35402095,2	MCF-7	breast:
3	chr6:35380537..35383478-chr6:35394277..35398227,3	K562	blood:
4	chr6:35388873..35391570-chr6:35394373..35396733,2	MCF-7	breast:
5	chr6:35390370..35392093-chr6:35395033..35397221,2	K562	blood:

Variant related genes	Relation type
ENSG00000065029	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1040436	0.91[CHD][hapmap]
rs1053049	0.81[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs1883322	0.88[CHD][hapmap]
rs2016520	0.93[CHD][hapmap];0.83[GIH][hapmap]
rs2038067	0.87[CEU][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2038068	0.88[CHD][hapmap];0.80[GIH][hapmap]
rs2076166	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076167	0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs2076168	0.81[ASN][1000 genomes]
rs2076169	0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2267665	0.88[CEU][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2267666	0.88[CHD][hapmap]
rs2267667	0.88[CHD][hapmap]
rs2267668	0.89[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2267669	0.89[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2395622	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2395623	0.81[ASN][1000 genomes]
rs2894401	0.83[CHD][hapmap];0.83[LWK][hapmap]
rs3734254	0.90[CHD][hapmap];0.80[GIH][hapmap];0.84[ASN][1000 genomes]
rs4713858	0.81[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs6457819	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6899536	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7749160	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7749165	0.83[AMR][1000 genomes]
rs7751481	0.88[CHD][hapmap]
rs9380506	0.81[ASN][1000 genomes]
rs9462082	0.88[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9462083	0.81[ASN][1000 genomes]
rs9462084	0.81[ASN][1000 genomes]
rs9470015	0.87[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9470024	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9794	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv462907	chr6:35333799-35408959	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv602908	chr6:35333799-35408959	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv602909	chr6:35356640-35423489	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats 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
5	nsv470812	chr6:35374461-35418118	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
7	nsv885799	chr6:35378778-35442397	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
8	nsv462908	chr6:35378778-35457396	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
9	nsv602910	chr6:35378778-35457396	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
10	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
11	nsv885800	chr6:35394247-35406153	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs760783	C6orf106	cis	cerebellum	SCAN
rs760783	PXT1	cis	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35383000-35396800	Weak transcription	Right Atrium	heart
2	chr6:35383400-35396600	Weak transcription	Stomach Mucosa	stomach
3	chr6:35383600-35402600	Weak transcription	Fetal Heart	heart
4	chr6:35389600-35396200	Strong transcription	Gastric	stomach
5	chr6:35391400-35396400	Strong transcription	Right Ventricle	heart
6	chr6:35391800-35396200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:35392400-35396600	Weak transcription	Small Intestine	intestine
8	chr6:35392400-35397200	Genic enhancers	NHLF	lung
9	chr6:35392600-35396200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:35392600-35396200	Enhancers	HUVEC	blood vessel
11	chr6:35392600-35402800	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:35393200-35396400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr6:35393200-35396400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:35393200-35397200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr6:35393400-35397000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:35393800-35396600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:35394000-35396200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:35394200-35396200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:35394200-35396200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:35394400-35396400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:35394400-35396400	ZNF genes & repeats	Lung	lung
22	chr6:35394600-35396400	Weak transcription	Brain Angular Gyrus	brain
23	chr6:35394600-35396400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:35394600-35396600	Weak transcription	Aorta	Aorta
25	chr6:35394600-35396600	Weak transcription	Fetal Lung	lung
26	chr6:35394600-35398200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
27	chr6:35394600-35403000	Weak transcription	Brain Germinal Matrix	brain
28	chr6:35394800-35396200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:35394800-35396200	Enhancers	HSMM	muscle
30	chr6:35394800-35396600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:35394800-35397000	Weak transcription	Brain Substantia Nigra	brain
32	chr6:35394800-35397000	ZNF genes & repeats	Esophagus	oesophagus
33	chr6:35395000-35396200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:35395000-35396400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:35395000-35396400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:35395000-35396400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:35395000-35396600	Weak transcription	Pancreas	Pancrea
38	chr6:35395000-35396600	Weak transcription	HSMMtube	muscle
39	chr6:35395000-35396600	Enhancers	NHDF-Ad	bronchial
40	chr6:35395000-35397200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:35395000-35398400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:35395000-35399800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:35395200-35396200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:35395200-35396200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr6:35395200-35396200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:35395200-35396400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr6:35395200-35396400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:35395200-35396400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr6:35395200-35396400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:35395200-35396600	Weak transcription	Brain Inferior Temporal Lobe	brain

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