Variant report

Variant	rs277369
Chromosome Location	chr1:75234661-75234662
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	chr1:75234170..75236486-chr1:75241343..75243331,2	K562	blood:
2	chr1:75228741..75231063-chr1:75233149..75235215,2	K562	blood:

Variant related genes	Relation type
ENSG00000162623	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1051122	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874122	1.00[ASN][1000 genomes]
rs10890142	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11485298	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11485555	0.87[ASN][1000 genomes]
rs12410060	1.00[ASN][1000 genomes]
rs1248244	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1409785	0.99[ASN][1000 genomes]
rs1465483	0.89[ASN][1000 genomes]
rs1475396	0.99[ASN][1000 genomes]
rs1969111	0.95[ASN][1000 genomes]
rs1980851	0.95[ASN][1000 genomes]
rs277368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277374	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277376	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277380	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277398	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277402	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2795030	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28482086	0.99[ASN][1000 genomes]
rs28568334	0.97[ASN][1000 genomes]
rs28583318	0.99[ASN][1000 genomes]
rs2881153	0.99[ASN][1000 genomes]
rs28857918	0.97[ASN][1000 genomes]
rs28879157	0.97[ASN][1000 genomes]
rs3806160	0.97[ASN][1000 genomes]
rs3819946	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3931020	1.00[ASN][1000 genomes]
rs405445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145871	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs438014	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs452242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs455032	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs525487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522428	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs968358	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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
rs277369	CRYZ	cis	Whole Blood	GTEx
rs277369	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs277369	CRYZ	cis	Artery Tibial	GTEx
rs277369	CRYZ	cis	Adipose Subcutaneous	GTEx
rs277369	CRYZ	cis	Lymphoblastoid	GTEx
rs277369	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs277369	CRYZ	cis	Nerve Tibial	GTEx
rs277369	CRYZ	cis	lung	GTEx
rs277369	CRYZ	cis	lesional skin	skin_eQTL
rs277369	CRYZ	cis	multi-tissue	Pritchard
rs277369	CRYZ	cis	Esophagus Mucosa	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75216000-75235200	Weak transcription	Right Ventricle	heart
2	chr1:75221400-75238000	Weak transcription	A549	lung
3	chr1:75221600-75237600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:75222200-75236000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:75223000-75235200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:75223600-75235200	Weak transcription	Spleen	Spleen
7	chr1:75225000-75235000	Weak transcription	Fetal Kidney	kidney
8	chr1:75226000-75237600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:75227800-75235600	Weak transcription	HUVEC	blood vessel
10	chr1:75228000-75235200	Weak transcription	Left Ventricle	heart
11	chr1:75228000-75235800	Weak transcription	Aorta	Aorta
12	chr1:75228400-75235000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:75230200-75234800	Weak transcription	GM12878-XiMat	blood
14	chr1:75230800-75238400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:75231200-75235200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:75231200-75235600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:75231200-75235800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:75231200-75237600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:75231200-75237600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:75231200-75237800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:75231200-75245600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:75231200-75246000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:75231400-75234800	Weak transcription	HSMMtube	muscle
24	chr1:75231600-75236200	Weak transcription	Primary B cells from cord blood	blood
25	chr1:75231800-75235000	Weak transcription	Dnd41	blood
26	chr1:75231800-75235800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:75231800-75237000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr1:75231800-75237400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:75232200-75238000	Weak transcription	Liver	Liver
30	chr1:75232600-75235000	Weak transcription	Primary T cells from cord blood	blood

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