Variant report

Variant	rs12793530
Chromosome Location	chr11:71161656-71161657
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr11:71161584-71161841	HepG2	liver:	n/a	n/a
2	FOXA1	chr11:71161549-71161855	HepG2	liver:	n/a	n/a
3	MYC	chr11:71160891-71161911	MCF10A-Er-Src	breast:	n/a	n/a
4	FOXA1	chr11:71161598-71161848	HepG2	liver:	n/a	n/a
5	FOXA1	chr11:71161494-71161934	HepG2	liver:	n/a	n/a
6	FOXA2	chr11:71161622-71161837	HepG2	liver:	n/a	n/a
7	MXI1	chr11:71158250-71161741	SK-N-SH	brain:	n/a	chr11:71159719-71159728 chr11:71159721-71159730 chr11:71159719-71159728
8	RXRA	chr11:71161542-71161826	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:71157940..71161417-chr11:71161465..71165970,9	K562	blood:
2	chr11:71159116..71165503-chr11:71274687..71279227,9	MCF-7	breast:
3	chr11:71156994..71165841-chr11:71185066..71202614,31	MCF-7	breast:

Variant related genes	Relation type
NADSYN1	TF binding region
DHCR7	TF binding region
ENSG00000172893	Chromatin interaction
ENSG00000254682	Chromatin interaction
ENSG00000172890	Chromatin interaction
ENSG00000204572	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1044482	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11233746	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233747	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11233789	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11546509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11600569	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600860	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11603330	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11604642	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11606033	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11606612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606631	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12278461	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12419279	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12419334	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12422045	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12785878	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12789751	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790010	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12790558	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12791871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12792306	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12793224	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12794668	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797951	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12800438	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12803256	0.80[ASN][1000 genomes]
rs12806844	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12807718	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12807827	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12808368	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1981412	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2002063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040323	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276360	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276361	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276362	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282620	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282621	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28364617	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2852853	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3750997	0.90[EUR][1000 genomes]
rs3794060	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4423214	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4488226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944062	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4944946	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944949	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944955	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944956	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944958	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944959	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944996	0.89[ASN][1000 genomes]
rs4945008	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs732934	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7928249	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7935125	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938885	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7944926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909217	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12793530	NADSYN1	cis	Thyroid	GTEx
rs12793530	RP11-660L16.2	cis	Whole Blood	GTEx
rs12793530	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12793530	RP11-660L16.2	cis	Thyroid	GTEx
rs12793530	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs12793530	RP11-660L16.2	cis	Heart Left Ventricle	GTEx
rs12793530	RP11-660L16.2	cis	Artery Aorta	GTEx
rs12793530	NADSYN1	cis	lung	GTEx
rs12793530	RP11-660L16.2	cis	Esophagus Muscularis	GTEx
rs12793530	RP11-660L16.2	cis	lung	GTEx
rs12793530	RP11-660L16.2	cis	Stomach	GTEx
rs12793530	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs12793530	NADSYN1	cis	Nerve Tibial	GTEx
rs12793530	RP11-660L16.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71158800-71162000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr11:71158800-71162000	Active TSS	GM12878-XiMat	blood
3	chr11:71160400-71161800	Flanking Active TSS	Dnd41	blood
4	chr11:71160400-71162800	Weak transcription	Gastric	stomach
5	chr11:71160400-71163000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:71160600-71161800	Enhancers	Adipose Nuclei	Adipose
7	chr11:71160600-71161800	Active TSS	Fetal Brain Female	brain
8	chr11:71160600-71162600	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr11:71160600-71162800	Enhancers	Primary B cells from cord blood	blood
10	chr11:71160600-71163000	Enhancers	Primary hematopoietic stem cells	blood
11	chr11:71160600-71163000	Weak transcription	Placenta	Placenta
12	chr11:71160600-71163000	Weak transcription	Left Ventricle	heart
13	chr11:71160600-71163000	Weak transcription	Right Atrium	heart
14	chr11:71160600-71163400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:71160600-71163400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:71160600-71163400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:71160600-71163400	Weak transcription	HSMMtube	muscle
18	chr11:71160800-71161800	Weak transcription	Brain Substantia Nigra	brain
19	chr11:71160800-71162200	Enhancers	Fetal Intestine Large	intestine
20	chr11:71160800-71162400	Weak transcription	Fetal Lung	lung
21	chr11:71160800-71162600	Enhancers	Brain Anterior Caudate	brain
22	chr11:71160800-71162600	Weak transcription	Fetal Kidney	kidney
23	chr11:71160800-71162600	Weak transcription	Lung	lung
24	chr11:71160800-71162600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr11:71160800-71162600	Weak transcription	NHDF-Ad	bronchial
26	chr11:71160800-71162800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:71160800-71162800	Weak transcription	Right Ventricle	heart
28	chr11:71160800-71163000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:71160800-71163000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr11:71160800-71163000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:71160800-71163000	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr11:71160800-71163000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:71160800-71163000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr11:71160800-71163000	Weak transcription	Esophagus	oesophagus
35	chr11:71160800-71163000	Weak transcription	Fetal Heart	heart
36	chr11:71160800-71163000	Weak transcription	Pancreas	Pancrea
37	chr11:71160800-71163000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr11:71160800-71163000	Weak transcription	Stomach Mucosa	stomach
39	chr11:71160800-71163000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr11:71160800-71163200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:71160800-71163200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:71160800-71163400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:71160800-71163400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr11:71160800-71163400	Enhancers	Fetal Intestine Small	intestine
45	chr11:71160800-71163400	Weak transcription	Ovary	ovary
46	chr11:71160800-71163600	Weak transcription	Aorta	Aorta
47	chr11:71161000-71161800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:71161000-71161800	Weak transcription	Brain Germinal Matrix	brain
49	chr11:71161000-71162000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr11:71161000-71162000	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links