Variant report

Variant	rs4949773
Chromosome Location	chr1:77633066-77633067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1010061	1.00[ASN][1000 genomes]
rs10443176	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518445	1.00[ASN][1000 genomes]
rs11162275	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162287	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11576574	1.00[ASN][1000 genomes]
rs11584919	1.00[CHD][hapmap]
rs12077763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12090495	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119019	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122553	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12123535	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126662	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132273	1.00[CHD][hapmap]
rs12141929	1.00[CHD][hapmap]
rs12143529	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562335	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1305486	1.00[ASN][1000 genomes]
rs1453981	1.00[CHD][hapmap]
rs1502525	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17100100	1.00[ASN][1000 genomes]
rs17100141	1.00[ASN][1000 genomes]
rs17100143	1.00[ASN][1000 genomes]
rs17100304	1.00[ASN][1000 genomes]
rs17368950	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1827448	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993266	1.00[ASN][1000 genomes]
rs2004962	1.00[ASN][1000 genomes]
rs41292260	1.00[ASN][1000 genomes]
rs41292264	1.00[ASN][1000 genomes]
rs4949772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949778	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949788	1.00[CHD][hapmap]
rs56666939	1.00[ASN][1000 genomes]
rs57267651	1.00[ASN][1000 genomes]
rs57389685	1.00[ASN][1000 genomes]
rs60792794	1.00[ASN][1000 genomes]
rs61782906	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6603937	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696605	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683932	1.00[ASN][1000 genomes]
rs72944757	1.00[ASN][1000 genomes]
rs73002568	1.00[ASN][1000 genomes]
rs73004429	1.00[ASN][1000 genomes]
rs73004430	1.00[ASN][1000 genomes]
rs73004434	1.00[ASN][1000 genomes]
rs7519485	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544099	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550325	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[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	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4949773	CRYZ	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77595400-77640400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:77606200-77651600	Weak transcription	Aorta	Aorta
3	chr1:77614400-77634000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:77614400-77634000	Weak transcription	Osteobl	bone
5	chr1:77614400-77635600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:77614400-77635600	Weak transcription	NHDF-Ad	bronchial
7	chr1:77616200-77663200	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:77617200-77636000	Weak transcription	HSMM	muscle
9	chr1:77618400-77633200	Weak transcription	Fetal Brain Male	brain
10	chr1:77618600-77634600	Weak transcription	Right Ventricle	heart
11	chr1:77619000-77638000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:77619000-77640200	Weak transcription	A549	lung
13	chr1:77620200-77633200	Weak transcription	Brain Angular Gyrus	brain
14	chr1:77621000-77641600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:77621800-77634000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:77622600-77633800	Weak transcription	HUVEC	blood vessel
17	chr1:77623200-77639400	Weak transcription	Fetal Lung	lung
18	chr1:77623400-77641000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr1:77625000-77634200	Weak transcription	Esophagus	oesophagus
20	chr1:77625600-77634600	Weak transcription	Pancreas	Pancrea
21	chr1:77625600-77637800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:77625800-77633400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:77625800-77635200	Weak transcription	Fetal Intestine Small	intestine
24	chr1:77625800-77640000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:77626000-77634000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:77626000-77635600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:77626000-77637800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:77626000-77639800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:77626000-77640600	Weak transcription	Brain Substantia Nigra	brain
30	chr1:77626000-77662600	Weak transcription	Thymus	Thymus
31	chr1:77626000-77684200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:77626200-77634000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:77626200-77634600	Weak transcription	Fetal Thymus	thymus
34	chr1:77626200-77637800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:77626200-77639400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:77626800-77639400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:77626800-77668000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:77626800-77674800	Weak transcription	Ovary	ovary
39	chr1:77626800-77676200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:77627200-77634000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:77627200-77638600	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:77627200-77641000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:77627800-77635600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:77628000-77634200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:77628000-77635800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:77628000-77636000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:77629000-77634000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:77629000-77637800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:77629000-77642000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:77629200-77634600	Weak transcription	Primary B cells from peripheral blood	blood

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