Variant report

Variant	rs2230493
Chromosome Location	chr3:53213657-53213658
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	chr3:53189150..53191553-chr3:53213309..53214973,2	MCF-7	breast:
2	chr3:53159175..53161619-chr3:53212406..53215272,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11130349	1.00[JPT][hapmap]
rs17052826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306570	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764111	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs6777221	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs73091417	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73091425	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73091435	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2230493	POC1A	cis	parietal	SCAN
rs2230493	C3orf54	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53197600-53227600	Weak transcription	Hela-S3	cervix
2	chr3:53197800-53214000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:53198000-53215600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:53200600-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:53201600-53228000	Weak transcription	NH-A	brain
6	chr3:53202000-53228400	Weak transcription	Fetal Kidney	kidney
7	chr3:53202800-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:53203200-53226800	Strong transcription	Fetal Stomach	stomach
9	chr3:53203600-53229800	Weak transcription	A549	lung
10	chr3:53205600-53229800	Weak transcription	Brain Angular Gyrus	brain
11	chr3:53205800-53213800	Weak transcription	Small Intestine	intestine
12	chr3:53206000-53213800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:53206000-53219400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:53206400-53216600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:53206400-53217000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:53206600-53215400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:53206600-53221400	Strong transcription	Fetal Intestine Small	intestine
18	chr3:53206800-53215600	Genic enhancers	Primary monocytes fromperipheralblood	blood
19	chr3:53206800-53219400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:53206800-53228000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:53207000-53214200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:53207200-53227400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:53207200-53227600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:53209000-53214000	Genic enhancers	GM12878-XiMat	blood
25	chr3:53209200-53222800	Weak transcription	Brain Germinal Matrix	brain
26	chr3:53209600-53228000	Weak transcription	HUVEC	blood vessel
27	chr3:53209600-53228400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:53210000-53229000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:53210600-53215800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:53210600-53228400	Strong transcription	Gastric	stomach
31	chr3:53210800-53215600	Weak transcription	HSMM	muscle
32	chr3:53211000-53227400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:53211200-53215600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:53211200-53217600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:53211400-53215600	Weak transcription	HSMMtube	muscle
36	chr3:53211400-53223000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:53211400-53227800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:53211600-53213800	Strong transcription	Fetal Muscle Leg	muscle
39	chr3:53211600-53224800	Strong transcription	Rectal Smooth Muscle	rectum
40	chr3:53211800-53214200	Genic enhancers	Primary B cells from cord blood	blood
41	chr3:53211800-53227800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:53212000-53214400	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:53212200-53214400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:53212200-53214400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr3:53212200-53216400	Genic enhancers	Primary B cells from peripheral blood	blood
46	chr3:53212200-53218000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:53212200-53221000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:53212200-53225200	Strong transcription	Right Ventricle	heart
49	chr3:53212200-53226200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:53212200-53226800	Strong transcription	Lung	lung

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