Variant report

Variant	rs28685856
Chromosome Location	chr1:75205344-75205345
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	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: 28 )
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];0.99[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];0.94[EUR][1000 genomes]
rs28602706	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28640981	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654603	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28767547	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28796389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28796647	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804435	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.95[EUR][1000 genomes]
rs3845357	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3889133	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55895041	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790736	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790737	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790739	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749690	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs28685856	TYW3	cis	Muscle Skeletal	GTEx
rs28685856	CRYZ	cis	Artery Tibial	GTEx
rs28685856	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs28685856	CRYZ	cis	Nerve Tibial	GTEx
rs28685856	CRYZ	cis	Whole Blood	GTEx
rs28685856	CRYZ	cis	lung	GTEx
rs28685856	CRYZ	cis	Artery Aorta	GTEx
rs28685856	CRYZ	cis	multi-tissue	Pritchard
rs28685856	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs28685856	CRYZ	cis	Adipose Subcutaneous	GTEx
rs28685856	CRYZ	cis	Esophagus Mucosa	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	chr1:75200200-75217600	Weak transcription	Stomach Mucosa	stomach
5	chr1:75200400-75210600	Weak transcription	Colonic Mucosa	Colon
6	chr1:75200400-75218400	Weak transcription	Fetal Heart	heart
7	chr1:75201000-75206000	Strong transcription	Fetal Lung	lung
8	chr1:75201200-75206200	Strong transcription	HSMM	muscle
9	chr1:75201200-75210600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:75201200-75212400	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:75201400-75212800	Strong transcription	Primary B cells from cord blood	blood
12	chr1:75201400-75231800	Strong transcription	Dnd41	blood
13	chr1:75201600-75206200	Strong transcription	HUVEC	blood vessel
14	chr1:75202000-75208600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:75202200-75207400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:75202200-75207800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:75202200-75209000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:75202400-75205400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:75202400-75205600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:75202400-75205800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:75202400-75206200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:75202400-75206200	Strong transcription	HSMMtube	muscle
23	chr1:75202400-75206400	Strong transcription	Brain Angular Gyrus	brain
24	chr1:75202400-75206600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:75202400-75207800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:75202400-75208000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:75202400-75208000	Strong transcription	K562	blood
28	chr1:75202400-75208400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr1:75202400-75208600	Strong transcription	Brain Substantia Nigra	brain
30	chr1:75202400-75209600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:75202400-75210000	Strong transcription	Fetal Thymus	thymus
32	chr1:75202400-75211400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:75202400-75212200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:75202400-75212800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:75202400-75212800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:75202400-75213000	Strong transcription	Liver	Liver
37	chr1:75202400-75219000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:75202400-75224000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:75202400-75226400	Strong transcription	Fetal Intestine Large	intestine
40	chr1:75202400-75231200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:75202400-75231200	Strong transcription	Adipose Nuclei	Adipose
42	chr1:75202400-75231200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr1:75202400-75231400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:75202600-75205800	Strong transcription	NHDF-Ad	bronchial
45	chr1:75202600-75206000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr1:75202600-75206400	Strong transcription	A549	lung
47	chr1:75202600-75207800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:75202600-75211000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:75202600-75212400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:75202600-75212400	Strong transcription	Stomach Smooth Muscle	stomach

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