Variant report

Variant	rs405445
Chromosome Location	chr1:75221150-75221151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:75220395..75222946-chr1:75225732..75227331,2	K562	blood:
2	chr1:75214596..75216328-chr1:75219166..75221198,2	K562	blood:

Variant related genes	Relation type
ENSG00000162623	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1051122	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874122	1.00[ASN][1000 genomes]
rs10890142	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11485298	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11485555	0.87[ASN][1000 genomes]
rs12410060	1.00[ASN][1000 genomes]
rs1248244	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1409785	0.99[ASN][1000 genomes]
rs1465483	0.89[ASN][1000 genomes]
rs1475396	0.99[ASN][1000 genomes]
rs1969111	0.95[ASN][1000 genomes]
rs1980851	0.95[ASN][1000 genomes]
rs277368	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277374	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277376	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277380	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277398	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277402	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2795030	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28482086	0.99[ASN][1000 genomes]
rs28568334	0.97[ASN][1000 genomes]
rs28583318	0.99[ASN][1000 genomes]
rs2881153	0.99[ASN][1000 genomes]
rs28857918	0.97[ASN][1000 genomes]
rs28879157	0.97[ASN][1000 genomes]
rs3806160	0.97[ASN][1000 genomes]
rs3819946	0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3931020	1.00[ASN][1000 genomes]
rs4145871	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs438014	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs452242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs455032	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs525487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522428	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs968358	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs405445	CRYZ	cis	lung	GTEx
rs405445	CRYZ	cis	Nerve Tibial	GTEx
rs405445	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs405445	CRYZ	cis	lymphoblastoid	seeQTL
rs405445	TYW3	cis	parietal	SCAN
rs405445	CRYZ	cis	cerebellum	SCAN
rs405445	CRYZ	cis	parietal	SCAN
rs405445	CRYZ	cis	Artery Tibial	GTEx
rs405445	TYW3	cis	cerebellum	SCAN
rs405445	CRYZ	cis	Adipose Subcutaneous	GTEx
rs405445	CRYZ	cis	Whole Blood	GTEx
rs405445	CRYZ	cis	Esophagus Mucosa	GTEx
rs405445	CRYZ	cis	multi-tissue	Pritchard
rs405445	CRYZ	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 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	chr1:75202400-75224000	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr1:75202400-75226400	Strong transcription	Fetal Intestine Large	intestine
5	chr1:75202400-75231200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:75202400-75231200	Strong transcription	Adipose Nuclei	Adipose
7	chr1:75202400-75231200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:75202400-75231400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:75202800-75222800	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:75202800-75225600	Strong transcription	Fetal Muscle Trunk	muscle
11	chr1:75204000-75221400	Weak transcription	Fetal Brain Male	brain
12	chr1:75204000-75221800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:75204000-75231400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:75204000-75231400	Weak transcription	Psoas Muscle	Psoas
15	chr1:75205200-75232400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:75205600-75221200	Strong transcription	Fetal Muscle Leg	muscle
17	chr1:75206200-75232400	Weak transcription	Small Intestine	intestine
18	chr1:75206200-75232800	Weak transcription	NHLF	lung
19	chr1:75206400-75221600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:75206800-75230600	Weak transcription	Pancreas	Pancrea
21	chr1:75206800-75233600	Weak transcription	Gastric	stomach
22	chr1:75207600-75222000	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:75207600-75233400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:75207800-75221200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr1:75209400-75228600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:75210600-75229000	Weak transcription	Brain Angular Gyrus	brain
27	chr1:75211000-75221600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:75211000-75222400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:75211000-75222600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:75211000-75232000	Weak transcription	Colonic Mucosa	Colon
31	chr1:75211200-75222400	Weak transcription	Esophagus	oesophagus
32	chr1:75211600-75221200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:75211600-75222400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr1:75211600-75222400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:75212000-75221200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:75213400-75227600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:75213600-75222000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:75213800-75222000	Strong transcription	Fetal Thymus	thymus
39	chr1:75214200-75222800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:75214400-75225400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr1:75214400-75225800	Strong transcription	Ovary	ovary
42	chr1:75214400-75228200	Strong transcription	Primary T cells from cord blood	blood
43	chr1:75214400-75232200	Strong transcription	Liver	Liver
44	chr1:75214600-75221400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:75214600-75221400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:75214600-75222800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:75214600-75222800	Strong transcription	Placenta	Placenta
48	chr1:75214600-75225000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr1:75214600-75225600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:75214600-75226400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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