Variant report

Variant	rs61790739
Chromosome Location	chr1:75216449-75216450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12129513	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1424671	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2345438	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535522	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28588069	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28594379	0.80[EUR][1000 genomes]
rs28602706	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28640981	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28654603	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685856	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695657	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28767547	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28796389	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28796647	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804435	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28831813	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497701	1.00[ASN][1000 genomes]
rs3845356	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3845357	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3889133	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55895041	1.00[ASN][1000 genomes]
rs61790736	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790737	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749690	0.96[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs61790739	CRYZ	cis	Nerve Tibial	GTEx
rs61790739	CRYZ	cis	Adipose Subcutaneous	GTEx
rs61790739	CRYZ	cis	lung	GTEx
rs61790739	TYW3	cis	Muscle Skeletal	GTEx
rs61790739	CRYZ	cis	Artery Aorta	GTEx
rs61790739	CRYZ	cis	Whole Blood	GTEx
rs61790739	CRYZ	cis	multi-tissue	Pritchard
rs61790739	CRYZ	cis	Esophagus Mucosa	GTEx
rs61790739	CRYZ	cis	Artery Tibial	GTEx
rs61790739	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs61790739	CRYZ	Cis_1M	lymphoblastoid	RTeQTL

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	chr1:75206000-75216800	Weak transcription	Fetal Kidney	kidney
23	chr1:75206000-75220400	Weak transcription	NHEK	skin
24	chr1:75206200-75218000	Weak transcription	Brain Germinal Matrix	brain
25	chr1:75206200-75220400	Weak transcription	HSMMtube	muscle
26	chr1:75206200-75232400	Weak transcription	Small Intestine	intestine
27	chr1:75206200-75232800	Weak transcription	NHLF	lung
28	chr1:75206400-75218400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:75206400-75219000	Weak transcription	A549	lung
30	chr1:75206400-75221600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:75206600-75216800	Weak transcription	NH-A	brain
32	chr1:75206600-75218600	Weak transcription	Osteobl	bone
33	chr1:75206800-75230600	Weak transcription	Pancreas	Pancrea
34	chr1:75206800-75233600	Weak transcription	Gastric	stomach
35	chr1:75207600-75222000	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:75207600-75233400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:75207800-75221200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:75208000-75218200	Weak transcription	K562	blood
39	chr1:75208200-75220000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:75209400-75228600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:75210600-75216800	Weak transcription	Fetal Brain Female	brain
42	chr1:75210600-75229000	Weak transcription	Brain Angular Gyrus	brain
43	chr1:75210800-75219400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:75210800-75220600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:75210800-75220600	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:75211000-75220400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:75211000-75221600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:75211000-75222400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:75211000-75222600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:75211000-75232000	Weak transcription	Colonic Mucosa	Colon

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