Variant report

Variant	rs2345438
Chromosome Location	chr1:75214193-75214194
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10161	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12125889	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12129513	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1424671	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1574941	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1590639	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17618340	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28535522	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28588069	0.80[EUR][1000 genomes]
rs28594379	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28602706	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28640981	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654603	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	1.00[ASN][1000 genomes]
rs28685856	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28695657	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28767547	0.82[AMR][1000 genomes]
rs28796389	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28796647	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28804435	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831813	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35497701	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845356	0.81[EUR][1000 genomes]
rs3845357	0.81[EUR][1000 genomes]
rs3889133	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55895041	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790736	1.00[ASN][1000 genomes]
rs61790737	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790739	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668736	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs749690	0.82[AMR][1000 genomes];0.81[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2345438	CRYZ	cis	Nerve Tibial	GTEx
rs2345438	CRYZ	cis	multi-tissue	Pritchard
rs2345438	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs2345438	CRYZ	cis	lung	GTEx
rs2345438	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs2345438	CRYZ	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:122 , 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	chr1:75200200-75217600	Weak transcription	Stomach Mucosa	stomach
3	chr1:75200400-75218400	Weak transcription	Fetal Heart	heart
4	chr1:75201400-75231800	Strong transcription	Dnd41	blood
5	chr1:75202400-75219000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:75202400-75224000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr1:75202400-75226400	Strong transcription	Fetal Intestine Large	intestine
8	chr1:75202400-75231200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:75202400-75231200	Strong transcription	Adipose Nuclei	Adipose
10	chr1:75202400-75231200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:75202400-75231400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:75202800-75222800	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:75202800-75225600	Strong transcription	Fetal Muscle Trunk	muscle
14	chr1:75204000-75218400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:75204000-75221400	Weak transcription	Fetal Brain Male	brain
16	chr1:75204000-75221800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:75204000-75231400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:75204000-75231400	Weak transcription	Psoas Muscle	Psoas
19	chr1:75204400-75217000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:75205200-75232400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:75205600-75221200	Strong transcription	Fetal Muscle Leg	muscle
22	chr1:75205800-75214200	Weak transcription	HMEC	breast
23	chr1:75205800-75214600	Weak transcription	NHDF-Ad	bronchial
24	chr1:75206000-75216800	Weak transcription	Fetal Kidney	kidney
25	chr1:75206000-75220400	Weak transcription	NHEK	skin
26	chr1:75206200-75214600	Weak transcription	Hela-S3	cervix
27	chr1:75206200-75218000	Weak transcription	Brain Germinal Matrix	brain
28	chr1:75206200-75220400	Weak transcription	HSMMtube	muscle
29	chr1:75206200-75232400	Weak transcription	Small Intestine	intestine
30	chr1:75206200-75232800	Weak transcription	NHLF	lung
31	chr1:75206400-75218400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:75206400-75219000	Weak transcription	A549	lung
33	chr1:75206400-75221600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:75206600-75216800	Weak transcription	NH-A	brain
35	chr1:75206600-75218600	Weak transcription	Osteobl	bone
36	chr1:75206800-75230600	Weak transcription	Pancreas	Pancrea
37	chr1:75206800-75233600	Weak transcription	Gastric	stomach
38	chr1:75207000-75214600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:75207600-75222000	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:75207600-75233400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:75207800-75214600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:75207800-75221200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:75208000-75218200	Weak transcription	K562	blood
44	chr1:75208200-75220000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:75209200-75214600	Weak transcription	Colon Smooth Muscle	Colon
46	chr1:75209400-75215400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:75209400-75228600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:75210600-75214200	Weak transcription	Brain Anterior Caudate	brain
49	chr1:75210600-75216800	Weak transcription	Fetal Brain Female	brain
50	chr1:75210600-75229000	Weak transcription	Brain Angular Gyrus	brain

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