Variant report

Variant	rs28804435
Chromosome Location	chr1:75208382-75208383
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10161	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12125889	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12129513	0.99[AMR][1000 genomes];0.90[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];0.92[EUR][1000 genomes]
rs1590639	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17618340	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2345438	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535522	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594379	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28602706	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28640981	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654603	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685856	0.82[AMR][1000 genomes];0.80[EUR][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];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28796647	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28831813	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497701	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889133	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55895041	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790736	1.00[ASN][1000 genomes]
rs61790737	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61790739	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6668736	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs749690	0.82[AMR][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
rs28804435	CRYZ	cis	Adipose Subcutaneous	GTEx
rs28804435	CRYZ	cis	multi-tissue	Pritchard
rs28804435	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs28804435	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs28804435	CRYZ	cis	Nerve Tibial	GTEx
rs28804435	CRYZ	cis	lung	GTEx

Chromatin state (count:123 , 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	chr1:75200400-75210600	Weak transcription	Colonic Mucosa	Colon
4	chr1:75200400-75218400	Weak transcription	Fetal Heart	heart
5	chr1:75201200-75210600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:75201200-75212400	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:75201400-75212800	Strong transcription	Primary B cells from cord blood	blood
8	chr1:75201400-75231800	Strong transcription	Dnd41	blood
9	chr1:75202000-75208600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:75202200-75209000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:75202400-75208400	Strong transcription	Duodenum Mucosa	Duodenum
12	chr1:75202400-75208600	Strong transcription	Brain Substantia Nigra	brain
13	chr1:75202400-75209600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:75202400-75210000	Strong transcription	Fetal Thymus	thymus
15	chr1:75202400-75211400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:75202400-75212200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:75202400-75212800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:75202400-75212800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:75202400-75213000	Strong transcription	Liver	Liver
20	chr1:75202400-75219000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:75202400-75224000	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr1:75202400-75226400	Strong transcription	Fetal Intestine Large	intestine
23	chr1:75202400-75231200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:75202400-75231200	Strong transcription	Adipose Nuclei	Adipose
25	chr1:75202400-75231200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:75202400-75231400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:75202600-75211000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:75202600-75212400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:75202600-75212400	Strong transcription	Stomach Smooth Muscle	stomach
30	chr1:75202800-75209000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:75202800-75209200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:75202800-75213000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:75202800-75222800	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:75202800-75225600	Strong transcription	Fetal Muscle Trunk	muscle
35	chr1:75203000-75208600	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:75203000-75211800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:75203000-75212800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:75203000-75213000	Strong transcription	Primary T cells from cord blood	blood
39	chr1:75203200-75209800	Strong transcription	Brain Hippocampus Middle	brain
40	chr1:75204000-75218400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:75204000-75221400	Weak transcription	Fetal Brain Male	brain
42	chr1:75204000-75221800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr1:75204000-75231400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:75204000-75231400	Weak transcription	Psoas Muscle	Psoas
45	chr1:75204400-75210200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:75204400-75217000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:75205000-75209000	Strong transcription	Esophagus	oesophagus
48	chr1:75205000-75210600	Strong transcription	Placenta	Placenta
49	chr1:75205000-75212600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:75205000-75213000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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