Variant report

Variant	rs28796647
Chromosome Location	chr1:75192338-75192339
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:75169904..75171834-chr1:75191758..75194711,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 11 )

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];1.00[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];0.93[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685856	0.92[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28767547	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28796389	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];1.00[ASN][1000 genomes]
rs28831813	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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];0.94[EUR][1000 genomes]
rs3845357	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[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	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790737	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790739	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749690	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs28796647	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs28796647	CRYZ	cis	Artery Tibial	GTEx
rs28796647	CRYZ	cis	Artery Aorta	GTEx
rs28796647	CRYZ	cis	Nerve Tibial	GTEx
rs28796647	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs28796647	CRYZ	cis	Whole Blood	GTEx
rs28796647	CRYZ	cis	Esophagus Mucosa	GTEx
rs28796647	CRYZ	cis	lung	GTEx
rs28796647	CRYZ	cis	Adipose Subcutaneous	GTEx
rs28796647	CRYZ	cis	multi-tissue	Pritchard
rs28796647	TYW3	cis	Muscle Skeletal	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75166600-75194800	Weak transcription	Esophagus	oesophagus
2	chr1:75167000-75197200	Weak transcription	Right Ventricle	heart
3	chr1:75171000-75197200	Weak transcription	Brain Angular Gyrus	brain
4	chr1:75174800-75198000	Weak transcription	Thymus	Thymus
5	chr1:75175400-75196000	Weak transcription	HSMMtube	muscle
6	chr1:75180000-75196000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:75180400-75197200	Weak transcription	Psoas Muscle	Psoas
8	chr1:75183000-75198400	Weak transcription	Fetal Brain Male	brain
9	chr1:75183800-75194000	Weak transcription	Fetal Heart	heart
10	chr1:75187200-75195400	Weak transcription	HMEC	breast
11	chr1:75187400-75197200	Weak transcription	Stomach Mucosa	stomach
12	chr1:75187800-75197200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:75188000-75194400	Weak transcription	Small Intestine	intestine
14	chr1:75188200-75195800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:75188200-75196000	Weak transcription	HSMM	muscle
16	chr1:75188200-75197200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:75188200-75198000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:75188400-75195400	Weak transcription	K562	blood
19	chr1:75188400-75196800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:75188400-75197200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:75188400-75198000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:75188800-75195000	ZNF genes & repeats	GM12878-XiMat	blood
23	chr1:75189000-75197200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:75189200-75196400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:75189400-75194400	Weak transcription	NHLF	lung
26	chr1:75189400-75194600	Weak transcription	Brain Substantia Nigra	brain
27	chr1:75189400-75194800	Weak transcription	Osteobl	bone
28	chr1:75189400-75195000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:75189400-75195400	Weak transcription	NHEK	skin
30	chr1:75189400-75195800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:75189400-75197200	Weak transcription	Left Ventricle	heart
32	chr1:75189400-75197400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:75189600-75192800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr1:75189600-75194200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:75189600-75194600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:75189600-75195800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:75189600-75195800	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:75189600-75195800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:75189600-75197200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:75189600-75197400	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:75189800-75195400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:75189800-75195600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:75189800-75196800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:75190000-75195800	Weak transcription	Fetal Kidney	kidney
45	chr1:75190400-75192400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:75190600-75194200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:75190600-75194600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:75190800-75192400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
49	chr1:75190800-75193000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:75190800-75194200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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