Variant report

Variant	rs1991839
Chromosome Location	chr4:124745047-124745048
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1016592	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13129313	1.00[CEU][hapmap]
rs2390590	0.86[ASN][1000 genomes]
rs3097909	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3097910	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3097913	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3097915	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3097916	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3097917	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3097918	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3097919	0.86[EUR][1000 genomes]
rs3097920	0.91[EUR][1000 genomes]
rs3113385	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3113396	0.89[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs6840618	1.00[CEU][hapmap]
rs721456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7654237	1.00[CEU][hapmap]
rs7699221	0.96[CEU][hapmap]
rs978534	0.93[AMR][1000 genomes];0.98[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	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv2754745	chr4:124698055-124770865	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1991839	TNIP3	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124735200-124753800	Weak transcription	Psoas Muscle	Psoas
2	chr4:124737600-124752200	Weak transcription	Gastric	stomach
3	chr4:124738400-124748000	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:124741000-124745400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:124741200-124745200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:124741200-124745200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:124741400-124746600	Weak transcription	NHDF-Ad	bronchial
8	chr4:124743200-124759800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr4:124743400-124745400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:124743400-124746600	Weak transcription	HMEC	breast
11	chr4:124743600-124746000	Weak transcription	Osteobl	bone
12	chr4:124743600-124751000	Weak transcription	Fetal Lung	lung
13	chr4:124743800-124745800	Weak transcription	NHLF	lung
14	chr4:124743800-124746400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:124743800-124746800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:124743800-124752000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:124743800-124752600	Weak transcription	Right Atrium	heart
18	chr4:124744000-124752400	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:124744400-124746000	Weak transcription	Fetal Intestine Small	intestine
20	chr4:124744400-124747000	Enhancers	HepG2	liver
21	chr4:124745000-124745400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:124745000-124749200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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