Variant report

Variant	rs1190790
Chromosome Location	chr6:131520289-131520290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10457568	0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs10457569	0.81[AMR][1000 genomes]
rs1190791	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190792	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1190793	0.93[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1190804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196463	0.90[JPT][hapmap];0.85[AMR][1000 genomes]
rs12196504	0.90[JPT][hapmap];0.82[AMR][1000 genomes]
rs12210171	0.90[JPT][hapmap]
rs12214638	0.90[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs12215812	0.90[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs1590356	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17652219	0.90[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs1923620	0.90[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs3777486	1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs3777488	0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs3777490	0.81[AMR][1000 genomes]
rs4404789	0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs6923644	0.90[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv830807	chr6:131390952-131581931	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv886665	chr6:131518894-131611309	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1190790	SNX17	trans	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131457600-131520800	Weak transcription	Right Ventricle	heart
2	chr6:131488200-131534800	Weak transcription	Gastric	stomach
3	chr6:131505000-131521000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:131505000-131521800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:131505200-131522600	Weak transcription	HSMMtube	muscle
6	chr6:131505800-131534600	Weak transcription	Brain Substantia Nigra	brain
7	chr6:131505800-131534800	Weak transcription	Pancreas	Pancrea
8	chr6:131506400-131520800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:131506600-131520600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:131506600-131520600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:131506600-131520600	Weak transcription	Spleen	Spleen
12	chr6:131506600-131520800	Weak transcription	Lung	lung
13	chr6:131506600-131523800	Weak transcription	HepG2	liver
14	chr6:131506600-131524000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:131506600-131529800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:131506600-131532000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:131506800-131551800	Weak transcription	Ovary	ovary
18	chr6:131507000-131520400	Weak transcription	Liver	Liver
19	chr6:131510400-131534800	Weak transcription	Small Intestine	intestine
20	chr6:131513000-131520800	Weak transcription	Aorta	Aorta
21	chr6:131513000-131520800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:131513000-131522600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr6:131513000-131523000	Weak transcription	Placenta	Placenta
24	chr6:131513200-131520600	Weak transcription	Left Ventricle	heart
25	chr6:131513200-131526400	Weak transcription	Fetal Intestine Small	intestine
26	chr6:131513200-131536400	Weak transcription	Esophagus	oesophagus
27	chr6:131513400-131520600	Weak transcription	Fetal Stomach	stomach
28	chr6:131514400-131529800	Weak transcription	Brain Germinal Matrix	brain
29	chr6:131514400-131541400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:131514600-131520600	Weak transcription	Fetal Lung	lung
31	chr6:131514600-131521200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:131514800-131520600	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:131516400-131520600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr6:131516600-131521200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:131517000-131520800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:131518200-131520800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr6:131518200-131520800	Enhancers	Primary T cells from cord blood	blood
38	chr6:131518200-131520800	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr6:131518200-131520800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:131518200-131521000	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr6:131518200-131521000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:131518200-131521200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:131518200-131525600	Weak transcription	Fetal Brain Male	brain
44	chr6:131518200-131531800	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:131518400-131520800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr6:131518400-131521000	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr6:131518400-131521000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr6:131518400-131522600	Enhancers	Primary hematopoietic stem cells	blood
49	chr6:131518600-131520600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:131518600-131520600	Weak transcription	Fetal Muscle Leg	muscle

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