Variant report

Variant	rs3819947
Chromosome Location	chr1:75229396-75229397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11162945	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1122338	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1133891	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11485264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11485299	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11487952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap]
rs12034724	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12043726	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13375787	0.85[CHB][hapmap]
rs1359750	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1581870	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032969	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes]
rs28374065	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445096	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28515016	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28563168	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28575168	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28719150	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28740807	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28804147	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28810187	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806161	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3819946	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs4650004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650005	0.84[AMR][1000 genomes]
rs4650007	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4650287	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4650288	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58715708	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60292279	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6681874	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs745108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535692	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768223	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9647	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv830259	chr1:75089177-75241062	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv1851105	chr1:75152186-75302921	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3819947	CRYZ	cis	lymphoblastoid	seeQTL
rs3819947	TYW3	cis	Artery Tibial	GTEx
rs3819947	TYW3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75200000-75231600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr1:75201400-75231800	Strong transcription	Dnd41	blood
3	chr1:75202400-75231200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:75202400-75231200	Strong transcription	Adipose Nuclei	Adipose
5	chr1:75202400-75231200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:75202400-75231400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:75204000-75231400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:75204000-75231400	Weak transcription	Psoas Muscle	Psoas
9	chr1:75205200-75232400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:75206200-75232400	Weak transcription	Small Intestine	intestine
11	chr1:75206200-75232800	Weak transcription	NHLF	lung
12	chr1:75206800-75230600	Weak transcription	Pancreas	Pancrea
13	chr1:75206800-75233600	Weak transcription	Gastric	stomach
14	chr1:75207600-75233400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:75211000-75232000	Weak transcription	Colonic Mucosa	Colon
16	chr1:75214400-75232200	Strong transcription	Liver	Liver
17	chr1:75215200-75231800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:75216000-75235200	Weak transcription	Right Ventricle	heart
19	chr1:75219200-75231000	Weak transcription	Lung	lung
20	chr1:75219200-75233400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:75219800-75232400	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:75219800-75232600	Weak transcription	K562	blood
23	chr1:75220000-75230600	Weak transcription	Fetal Heart	heart
24	chr1:75220000-75231000	Weak transcription	Hela-S3	cervix
25	chr1:75220800-75230800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:75221400-75231800	Weak transcription	NHDF-Ad	bronchial
27	chr1:75221400-75232400	Weak transcription	NHEK	skin
28	chr1:75221400-75238000	Weak transcription	A549	lung
29	chr1:75221600-75229600	Weak transcription	NH-A	brain
30	chr1:75221600-75229800	Weak transcription	HSMMtube	muscle
31	chr1:75221600-75234600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:75221600-75237600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:75222200-75230600	Weak transcription	Brain Substantia Nigra	brain
34	chr1:75222200-75236000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:75222600-75230200	Strong transcription	GM12878-XiMat	blood
36	chr1:75223000-75231200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:75223000-75231200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:75223000-75232600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:75223000-75232800	Weak transcription	Esophagus	oesophagus
40	chr1:75223000-75235200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:75223200-75230400	Weak transcription	Brain Anterior Caudate	brain
42	chr1:75223200-75231000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:75223200-75231400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:75223200-75231800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:75223200-75232200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:75223200-75232600	Weak transcription	Fetal Brain Female	brain
47	chr1:75223200-75232800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:75223200-75233400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:75223600-75231000	Weak transcription	Brain Germinal Matrix	brain
50	chr1:75223600-75232800	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links