Variant report

Variant	rs28683801
Chromosome Location	chr1:75211738-75211739
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	chr1:75198016..75202216-chr1:75208581..75212721,6	K562	blood:
2	chr1:75198820..75201611-chr1:75210019..75212215,2	K562	blood:

Variant related genes	Relation type
ENSG00000162623	Chromatin interaction
ENSG00000116791	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12129513	1.00[ASN][1000 genomes]
rs1424671	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2345438	1.00[ASN][1000 genomes]
rs28535522	1.00[ASN][1000 genomes]
rs28588069	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28602706	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28640981	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654603	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685856	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695657	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28767547	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28796389	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28796647	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804435	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831813	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497701	1.00[ASN][1000 genomes]
rs3845356	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3845357	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3889133	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55895041	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790736	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790737	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790739	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749690	0.96[AFR][1000 genomes];0.96[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	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
rs28683801	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs28683801	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs28683801	CRYZ	cis	Nerve Tibial	GTEx
rs28683801	CRYZ	cis	lung	GTEx
rs28683801	CRYZ	cis	Esophagus Mucosa	GTEx
rs28683801	TYW3	cis	Muscle Skeletal	GTEx
rs28683801	CRYZ	cis	multi-tissue	Pritchard
rs28683801	CRYZ	cis	Artery Aorta	GTEx
rs28683801	CRYZ	cis	Adipose Subcutaneous	GTEx
rs28683801	CRYZ	cis	Whole Blood	GTEx
rs28683801	CRYZ	cis	Artery Tibial	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	chr1:75201200-75212400	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:75201400-75212800	Strong transcription	Primary B cells from cord blood	blood
6	chr1:75201400-75231800	Strong transcription	Dnd41	blood
7	chr1:75202400-75212200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:75202400-75212800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:75202400-75212800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:75202400-75213000	Strong transcription	Liver	Liver
11	chr1:75202400-75219000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:75202400-75224000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr1:75202400-75226400	Strong transcription	Fetal Intestine Large	intestine
14	chr1:75202400-75231200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:75202400-75231200	Strong transcription	Adipose Nuclei	Adipose
16	chr1:75202400-75231200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:75202400-75231400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:75202600-75212400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:75202600-75212400	Strong transcription	Stomach Smooth Muscle	stomach
20	chr1:75202800-75213000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:75202800-75222800	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:75202800-75225600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:75203000-75211800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:75203000-75212800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr1:75203000-75213000	Strong transcription	Primary T cells from cord blood	blood
26	chr1:75204000-75218400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:75204000-75221400	Weak transcription	Fetal Brain Male	brain
28	chr1:75204000-75221800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:75204000-75231400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:75204000-75231400	Weak transcription	Psoas Muscle	Psoas
31	chr1:75204400-75217000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:75205000-75212600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:75205000-75213000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:75205000-75213000	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr1:75205000-75213200	Strong transcription	Left Ventricle	heart
36	chr1:75205200-75232400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:75205600-75221200	Strong transcription	Fetal Muscle Leg	muscle
38	chr1:75205800-75214200	Weak transcription	HMEC	breast
39	chr1:75205800-75214600	Weak transcription	NHDF-Ad	bronchial
40	chr1:75206000-75216800	Weak transcription	Fetal Kidney	kidney
41	chr1:75206000-75220400	Weak transcription	NHEK	skin
42	chr1:75206200-75212000	Weak transcription	HSMM	muscle
43	chr1:75206200-75214600	Weak transcription	Hela-S3	cervix
44	chr1:75206200-75218000	Weak transcription	Brain Germinal Matrix	brain
45	chr1:75206200-75220400	Weak transcription	HSMMtube	muscle
46	chr1:75206200-75232400	Weak transcription	Small Intestine	intestine
47	chr1:75206200-75232800	Weak transcription	NHLF	lung
48	chr1:75206400-75212800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr1:75206400-75218400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:75206400-75219000	Weak transcription	A549	lung

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