Variant report

Variant	rs2412500
Chromosome Location	chr4:54643909-54643910
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	chr4:54637798..54639736-chr4:54642892..54644483,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1013508	0.95[ASN][1000 genomes]
rs1013509	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11133287	0.95[ASN][1000 genomes]
rs11721806	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11723162	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11731952	0.96[ASN][1000 genomes]
rs11734520	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12646885	0.95[ASN][1000 genomes]
rs1498815	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1498816	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1498829	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1874915	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2102011	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2412491	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412492	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412496	0.95[ASN][1000 genomes]
rs2412498	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4495107	0.91[ASN][1000 genomes]
rs4501282	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4561980	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4864821	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56061807	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60681996	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62297730	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62297732	0.97[ASN][1000 genomes]
rs67780867	0.95[ASN][1000 genomes]
rs6819547	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6819611	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6827313	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6827952	0.87[ASN][1000 genomes]
rs6834410	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6837405	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6837817	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6842213	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6842407	0.94[ASN][1000 genomes]
rs6843127	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6845180	0.88[ASN][1000 genomes]
rs6845286	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6846594	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6850939	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6854881	0.89[ASN][1000 genomes]
rs6858638	0.91[ASN][1000 genomes]
rs7686706	0.95[ASN][1000 genomes]
rs7688892	0.96[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	nsv879015	chr4:54596466-54665559	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv879016	chr4:54638218-54710952	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2412500	TXNDC9	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54642800-54644800	Enhancers	NHLF	lung
2	chr4:54642800-54645400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:54643000-54645200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:54643200-54644000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:54643200-54644000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:54643200-54644000	Enhancers	NH-A	brain
7	chr4:54643200-54644600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr4:54643200-54644600	Enhancers	NHEK	skin
9	chr4:54643200-54644800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:54643200-54645200	Enhancers	Osteobl	bone
11	chr4:54643400-54644000	Enhancers	HSMM	muscle
12	chr4:54643400-54644200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:54643400-54644600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:54643400-54644800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:54643400-54644800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:54643400-54645200	Enhancers	Fetal Stomach	stomach
17	chr4:54643400-54645400	Enhancers	NHDF-Ad	bronchial
18	chr4:54643600-54644000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr4:54643600-54644000	Flanking Active TSS	HMEC	breast
20	chr4:54643600-54644200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:54643600-54644600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:54643800-54644000	Flanking Active TSS	A549	lung
23	chr4:54643800-54647400	Weak transcription	Liver	Liver

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