Variant report

Variant	rs28535522
Chromosome Location	chr1:75181345-75181346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10161	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12125889	0.95[AMR][1000 genomes]
rs12129513	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[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];0.85[EUR][1000 genomes]
rs1590639	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17618340	0.88[AMR][1000 genomes]
rs2345438	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594379	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28602706	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28640981	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654603	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	1.00[ASN][1000 genomes]
rs28685856	0.82[AMR][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];1.00[ASN][1000 genomes]
rs28796647	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28804435	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831813	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35497701	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889133	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55895041	0.98[AMR][1000 genomes];0.93[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]
rs749690	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv871152	chr1:75152186-75197533	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	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
rs28535522	CRYZ	cis	Adipose Subcutaneous	GTEx
rs28535522	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs28535522	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs28535522	CRYZ	cis	lung	GTEx
rs28535522	CRYZ	cis	Nerve Tibial	GTEx
rs28535522	CRYZ	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75156000-75183400	Weak transcription	Fetal Heart	heart
2	chr1:75159400-75187400	Weak transcription	NHEK	skin
3	chr1:75166200-75183800	Weak transcription	Brain Anterior Caudate	brain
4	chr1:75166400-75191400	Weak transcription	Placenta	Placenta
5	chr1:75166600-75182800	Weak transcription	HSMM	muscle
6	chr1:75166600-75194800	Weak transcription	Esophagus	oesophagus
7	chr1:75166800-75189200	Weak transcription	Spleen	Spleen
8	chr1:75167000-75197200	Weak transcription	Right Ventricle	heart
9	chr1:75167400-75181800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:75167600-75190600	Strong transcription	Liver	Liver
11	chr1:75167600-75190800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:75167800-75190000	Strong transcription	Adipose Nuclei	Adipose
13	chr1:75168600-75187000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:75168800-75186400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:75169000-75182200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:75169000-75189600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:75169400-75182800	Weak transcription	HUVEC	blood vessel
18	chr1:75169400-75190600	Strong transcription	Primary B cells from cord blood	blood
19	chr1:75169400-75191600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:75169600-75184600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:75169800-75191800	Weak transcription	Colonic Mucosa	Colon
22	chr1:75170000-75183600	Weak transcription	Fetal Kidney	kidney
23	chr1:75170400-75189600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:75170600-75181800	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:75170600-75184400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:75170600-75184600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:75170600-75187000	Weak transcription	Stomach Mucosa	stomach
28	chr1:75170600-75187200	Weak transcription	Small Intestine	intestine
29	chr1:75170800-75187200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:75171000-75197200	Weak transcription	Brain Angular Gyrus	brain
31	chr1:75171800-75189800	Strong transcription	HepG2	liver
32	chr1:75172000-75189400	Strong transcription	Fetal Muscle Leg	muscle
33	chr1:75172600-75182000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:75172600-75183200	Weak transcription	Dnd41	blood
35	chr1:75172600-75185600	Weak transcription	Fetal Thymus	thymus
36	chr1:75172600-75185800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:75172800-75184200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:75173200-75182400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:75173400-75189200	Strong transcription	Ovary	ovary
40	chr1:75173400-75189600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:75173600-75189600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:75173800-75184600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:75174600-75189600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr1:75174800-75198000	Weak transcription	Thymus	Thymus
45	chr1:75175200-75183600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:75175400-75184600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr1:75175400-75187600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:75175400-75196000	Weak transcription	HSMMtube	muscle
49	chr1:75175800-75183200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:75176400-75189400	Strong transcription	Primary T cells from cord blood	blood

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