Variant report

Variant	rs12476558
Chromosome Location	chr2:128243139-128243140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:128241495..128243616-chr2:128253341..128255366,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10432384	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10460269	0.83[AMR][1000 genomes]
rs10928770	0.83[AMR][1000 genomes]
rs11694581	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12463949	0.90[ASN][1000 genomes]
rs12464981	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12466957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12475191	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12475389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13013022	0.80[AMR][1000 genomes]
rs13026187	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1864553	0.88[CEU][hapmap]
rs1968396	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2052953	0.80[ASN][1000 genomes]
rs2099209	0.85[MEX][hapmap]
rs2303947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732207	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4662733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7590705	0.94[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs777556	0.88[CEU][hapmap]
rs873099	0.88[CEU][hapmap];0.85[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12476558	ERCC3	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128223600-128268800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:128226200-128244000	Weak transcription	Psoas Muscle	Psoas
3	chr2:128229000-128257000	Weak transcription	Stomach Mucosa	stomach
4	chr2:128235200-128270000	Strong transcription	Dnd41	blood
5	chr2:128237200-128243400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:128237200-128244000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:128237400-128252400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr2:128237400-128262400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:128237600-128243400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:128237600-128243600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:128237600-128243800	Strong transcription	Duodenum Mucosa	Duodenum
12	chr2:128237600-128243800	Strong transcription	Osteobl	bone
13	chr2:128237600-128244000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:128237600-128244600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:128237600-128244800	Strong transcription	Esophagus	oesophagus
16	chr2:128237600-128246600	Strong transcription	Fetal Stomach	stomach
17	chr2:128237600-128247200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:128237600-128247600	Strong transcription	Thymus	Thymus
19	chr2:128237600-128248000	Strong transcription	Fetal Intestine Large	intestine
20	chr2:128237600-128251400	Strong transcription	Rectal Smooth Muscle	rectum
21	chr2:128237600-128252200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:128237600-128252200	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:128237600-128255000	Strong transcription	Fetal Muscle Leg	muscle
24	chr2:128237600-128255200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr2:128237600-128255400	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:128237600-128256000	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:128237600-128256200	Strong transcription	HepG2	liver
28	chr2:128237600-128263200	Strong transcription	Adipose Nuclei	Adipose
29	chr2:128237600-128263200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr2:128237600-128263400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:128237600-128263400	Strong transcription	Fetal Thymus	thymus
32	chr2:128237800-128243400	Strong transcription	Primary B cells from cord blood	blood
33	chr2:128237800-128243400	Strong transcription	Lung	lung
34	chr2:128237800-128248600	Strong transcription	Colonic Mucosa	Colon
35	chr2:128237800-128252400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:128237800-128252400	Strong transcription	Left Ventricle	heart
37	chr2:128237800-128252400	Strong transcription	GM12878-XiMat	blood
38	chr2:128237800-128254400	Strong transcription	Brain Substantia Nigra	brain
39	chr2:128237800-128254600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:128237800-128255800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr2:128237800-128263200	Strong transcription	Liver	Liver
42	chr2:128237800-128263200	Strong transcription	HUVEC	blood vessel
43	chr2:128237800-128263400	Strong transcription	Placenta	Placenta
44	chr2:128238400-128244000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:128238400-128255200	Strong transcription	K562	blood
46	chr2:128238400-128262400	Strong transcription	NH-A	brain
47	chr2:128238800-128248200	Strong transcription	Ovary	ovary
48	chr2:128238800-128260400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr2:128239000-128244000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr2:128239000-128246400	Strong transcription	Fetal Intestine Small	intestine

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