Variant report

Variant	rs277375
Chromosome Location	chr1:75204143-75204144
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	chr1:75197640..75200637-chr1:75200867..75204722,5	MCF-7	breast:
2	chr1:75197578..75200968-chr1:75201632..75206969,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162623	Chromatin interaction
ENSG00000116791	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1051122	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10874122	0.98[ASN][1000 genomes]
rs10890142	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11485298	0.97[ASN][1000 genomes]
rs11485555	0.87[ASN][1000 genomes]
rs12410060	0.98[ASN][1000 genomes]
rs1248244	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1409785	0.97[ASN][1000 genomes]
rs1465483	0.91[ASN][1000 genomes]
rs1475396	0.97[ASN][1000 genomes]
rs1969111	0.93[ASN][1000 genomes]
rs1980851	0.93[ASN][1000 genomes]
rs277368	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277369	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]
rs277374	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277376	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277380	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277398	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277402	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2795030	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28482086	0.97[ASN][1000 genomes]
rs28568334	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28583318	0.97[ASN][1000 genomes]
rs2881153	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28857918	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28879157	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3806160	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3819946	0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3931020	0.98[ASN][1000 genomes]
rs405445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4145871	0.97[ASN][1000 genomes]
rs438014	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs455032	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs525487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7522428	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs968358	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs277375	CRYZ	cis	Whole Blood	GTEx
rs277375	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs277375	CRYZ	cis	Artery Tibial	GTEx
rs277375	CRYZ	cis	multi-tissue	Pritchard
rs277375	CRYZ	cis	Esophagus Mucosa	GTEx
rs277375	CRYZ	cis	lung	GTEx
rs277375	CRYZ	cis	Nerve Tibial	GTEx
rs277375	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs277375	CRYZ	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75199600-75206000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:75199800-75207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:75200000-75231600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr1:75200200-75205200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:75200200-75217600	Weak transcription	Stomach Mucosa	stomach
6	chr1:75200400-75210600	Weak transcription	Colonic Mucosa	Colon
7	chr1:75200400-75218400	Weak transcription	Fetal Heart	heart
8	chr1:75201000-75206000	Strong transcription	Fetal Lung	lung
9	chr1:75201200-75206200	Strong transcription	HSMM	muscle
10	chr1:75201200-75210600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:75201200-75212400	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:75201400-75212800	Strong transcription	Primary B cells from cord blood	blood
13	chr1:75201400-75231800	Strong transcription	Dnd41	blood
14	chr1:75201600-75206200	Strong transcription	HUVEC	blood vessel
15	chr1:75202000-75208600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:75202200-75204200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:75202200-75205000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:75202200-75207400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr1:75202200-75207800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:75202200-75209000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:75202400-75204400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:75202400-75204400	Strong transcription	NHEK	skin
23	chr1:75202400-75204600	Strong transcription	Brain Anterior Caudate	brain
24	chr1:75202400-75205400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:75202400-75205600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:75202400-75205800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:75202400-75206200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:75202400-75206200	Strong transcription	HSMMtube	muscle
29	chr1:75202400-75206400	Strong transcription	Brain Angular Gyrus	brain
30	chr1:75202400-75206600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:75202400-75207800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:75202400-75208000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:75202400-75208000	Strong transcription	K562	blood
34	chr1:75202400-75208400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:75202400-75208600	Strong transcription	Brain Substantia Nigra	brain
36	chr1:75202400-75209600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:75202400-75210000	Strong transcription	Fetal Thymus	thymus
38	chr1:75202400-75211400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:75202400-75212200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:75202400-75212800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:75202400-75212800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:75202400-75213000	Strong transcription	Liver	Liver
43	chr1:75202400-75219000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:75202400-75224000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr1:75202400-75226400	Strong transcription	Fetal Intestine Large	intestine
46	chr1:75202400-75231200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:75202400-75231200	Strong transcription	Adipose Nuclei	Adipose
48	chr1:75202400-75231200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr1:75202400-75231400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:75202600-75205800	Strong transcription	NHDF-Ad	bronchial

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