Variant report

Variant	rs3819946
Chromosome Location	chr1:75175886-75175887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1051122	0.91[ASN][1000 genomes]
rs10874122	0.83[ASN][1000 genomes]
rs10890142	0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1122338	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1133891	0.80[CHD][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes]
rs11485264	0.80[CHD][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11485298	0.84[ASN][1000 genomes]
rs11485555	0.86[ASN][1000 genomes]
rs11487952	0.81[GIH][hapmap]
rs12410060	0.83[ASN][1000 genomes]
rs1248244	0.82[ASN][1000 genomes]
rs1409785	0.84[ASN][1000 genomes]
rs1465483	0.90[ASN][1000 genomes]
rs1475396	0.84[ASN][1000 genomes]
rs1969111	0.81[ASN][1000 genomes]
rs1980851	0.81[ASN][1000 genomes]
rs2032969	0.84[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs277368	0.88[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs277369	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs277374	0.88[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs277375	0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs277376	0.83[ASN][1000 genomes]
rs277396	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs277398	0.85[ASN][1000 genomes]
rs277402	0.88[ASN][1000 genomes]
rs2795030	0.83[ASN][1000 genomes]
rs28374065	0.81[AMR][1000 genomes]
rs28482086	0.84[ASN][1000 genomes]
rs28515016	0.82[AMR][1000 genomes]
rs28563168	0.86[AMR][1000 genomes]
rs28568334	0.86[ASN][1000 genomes]
rs28575168	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28583318	0.84[ASN][1000 genomes]
rs28719150	0.85[AMR][1000 genomes]
rs28740807	0.83[AMR][1000 genomes]
rs28804147	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28810187	0.84[AMR][1000 genomes]
rs2881153	0.84[ASN][1000 genomes]
rs28857918	0.86[ASN][1000 genomes]
rs28879157	0.86[ASN][1000 genomes]
rs3806160	0.86[ASN][1000 genomes]
rs3806161	0.84[AMR][1000 genomes]
rs3819947	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs3931020	0.83[ASN][1000 genomes]
rs405445	0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4145871	0.84[ASN][1000 genomes]
rs438014	0.85[ASN][1000 genomes]
rs452242	0.88[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs455032	0.91[ASN][1000 genomes]
rs4650287	0.86[AMR][1000 genomes]
rs4650288	0.85[AMR][1000 genomes]
rs525487	0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs60292279	0.86[AMR][1000 genomes]
rs745108	0.85[AMR][1000 genomes]
rs7522428	0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs768223	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs968358	0.91[ASN][1000 genomes]

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	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	nsv871152	chr1:75152186-75197533	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3819946	CRYZ	cis	Lymphoblastoid	GTEx
rs3819946	CRYZ	cis	lymphoblastoid	seeQTL
rs3819946	TYW3	cis	Heart Left Ventricle	GTEx
rs3819946	TYW3	cis	Artery Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75141800-75179600	Weak transcription	Aorta	Aorta
2	chr1:75156000-75183400	Weak transcription	Fetal Heart	heart
3	chr1:75159400-75187400	Weak transcription	NHEK	skin
4	chr1:75159800-75176600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:75164000-75176600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:75164000-75176600	Weak transcription	Fetal Stomach	stomach
7	chr1:75164200-75178600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:75164800-75178400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:75165000-75176600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:75166200-75183800	Weak transcription	Brain Anterior Caudate	brain
11	chr1:75166400-75191400	Weak transcription	Placenta	Placenta
12	chr1:75166600-75182800	Weak transcription	HSMM	muscle
13	chr1:75166600-75194800	Weak transcription	Esophagus	oesophagus
14	chr1:75166800-75176600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:75166800-75176600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:75166800-75176600	Weak transcription	Gastric	stomach
17	chr1:75166800-75189200	Weak transcription	Spleen	Spleen
18	chr1:75167000-75181000	Weak transcription	Lung	lung
19	chr1:75167000-75197200	Weak transcription	Right Ventricle	heart
20	chr1:75167200-75178000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:75167400-75181800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:75167600-75176800	Weak transcription	NHLF	lung
23	chr1:75167600-75190600	Strong transcription	Liver	Liver
24	chr1:75167600-75190800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:75167800-75179600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:75167800-75190000	Strong transcription	Adipose Nuclei	Adipose
27	chr1:75168000-75177800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr1:75168200-75177400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:75168600-75177000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:75168600-75181200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:75168600-75187000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:75168800-75186400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:75169000-75176600	Weak transcription	Pancreas	Pancrea
34	chr1:75169000-75178000	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:75169000-75178600	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:75169000-75182200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:75169000-75189600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:75169400-75182800	Weak transcription	HUVEC	blood vessel
39	chr1:75169400-75190600	Strong transcription	Primary B cells from cord blood	blood
40	chr1:75169400-75191600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:75169600-75178400	Strong transcription	GM12878-XiMat	blood
42	chr1:75169600-75184600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:75169800-75191800	Weak transcription	Colonic Mucosa	Colon
44	chr1:75170000-75183600	Weak transcription	Fetal Kidney	kidney
45	chr1:75170200-75176600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:75170400-75176800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:75170400-75189600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:75170600-75176200	Weak transcription	Brain Substantia Nigra	brain
49	chr1:75170600-75176600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:75170600-75176800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links