Variant report

Variant	rs28796389
Chromosome Location	chr1:75207320-75207321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs12129513	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1424671	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2345438	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28535522	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28588069	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28602706	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28640981	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654603	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28767547	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28796647	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804435	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831813	1.00[AFR][1000 genomes];1.00[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];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3845357	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3889133	0.82[AMR][1000 genomes];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];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790737	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790739	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749690	0.96[AFR][1000 genomes];0.98[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs28796389	CRYZ	cis	lung	GTEx
rs28796389	CRYZ	cis	Nerve Tibial	GTEx
rs28796389	CRYZ	cis	Esophagus Mucosa	GTEx
rs28796389	CRYZ	cis	Artery Tibial	GTEx
rs28796389	CRYZ	cis	Artery Aorta	GTEx
rs28796389	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs28796389	TYW3	cis	Muscle Skeletal	GTEx
rs28796389	CRYZ	cis	Whole Blood	GTEx
rs28796389	CRYZ	cis	Adipose Subcutaneous	GTEx
rs28796389	CRYZ	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75199800-75207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:75200000-75231600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:75200200-75217600	Weak transcription	Stomach Mucosa	stomach
4	chr1:75200400-75210600	Weak transcription	Colonic Mucosa	Colon
5	chr1:75200400-75218400	Weak transcription	Fetal Heart	heart
6	chr1:75201200-75210600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:75201200-75212400	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:75201400-75212800	Strong transcription	Primary B cells from cord blood	blood
9	chr1:75201400-75231800	Strong transcription	Dnd41	blood
10	chr1:75202000-75208600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:75202200-75207400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:75202200-75207800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:75202200-75209000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:75202400-75207800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:75202400-75208000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:75202400-75208000	Strong transcription	K562	blood
17	chr1:75202400-75208400	Strong transcription	Duodenum Mucosa	Duodenum
18	chr1:75202400-75208600	Strong transcription	Brain Substantia Nigra	brain
19	chr1:75202400-75209600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:75202400-75210000	Strong transcription	Fetal Thymus	thymus
21	chr1:75202400-75211400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:75202400-75212200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:75202400-75212800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:75202400-75212800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:75202400-75213000	Strong transcription	Liver	Liver
26	chr1:75202400-75219000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:75202400-75224000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:75202400-75226400	Strong transcription	Fetal Intestine Large	intestine
29	chr1:75202400-75231200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:75202400-75231200	Strong transcription	Adipose Nuclei	Adipose
31	chr1:75202400-75231200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:75202400-75231400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:75202600-75207800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:75202600-75211000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:75202600-75212400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:75202600-75212400	Strong transcription	Stomach Smooth Muscle	stomach
37	chr1:75202800-75207600	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:75202800-75208200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:75202800-75209000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:75202800-75209200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:75202800-75213000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:75202800-75222800	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:75202800-75225600	Strong transcription	Fetal Muscle Trunk	muscle
44	chr1:75203000-75208600	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:75203000-75211800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:75203000-75212800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:75203000-75213000	Strong transcription	Primary T cells from cord blood	blood
48	chr1:75203200-75209800	Strong transcription	Brain Hippocampus Middle	brain
49	chr1:75204000-75218400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr1:75204000-75221400	Weak transcription	Fetal Brain Male	brain

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