Variant report

Variant	rs2844672
Chromosome Location	chr6:31005139-31005140
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	chr6:30990191..30992901-chr6:31003159..31005249,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs2252195	0.80[AFR][1000 genomes]
rs2394424	0.80[AFR][1000 genomes]
rs2394428	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2394429	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2394430	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517538	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2517539	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517543	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517548	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517550	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517551	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517552	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523870	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2523872	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523873	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523874	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844665	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844669	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844681	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844683	0.86[EUR][1000 genomes]
rs3131927	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2844672	TCF19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31003400-31006200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:31003600-31005800	Enhancers	Hela-S3	cervix
3	chr6:31003800-31005800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:31004000-31005800	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr6:31004000-31006000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:31004200-31005400	Enhancers	Psoas Muscle	Psoas
7	chr6:31004400-31005200	Enhancers	Osteobl	bone
8	chr6:31004400-31005600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:31004400-31006000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:31004400-31006000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:31004400-31006000	Enhancers	Pancreas	Pancrea
12	chr6:31004400-31007800	Enhancers	Stomach Mucosa	stomach
13	chr6:31004400-31010800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:31004800-31005200	Enhancers	Left Ventricle	heart
15	chr6:31004800-31005400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:31004800-31005600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr6:31004800-31006000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:31004800-31006000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:31004800-31006000	Enhancers	Lung	lung
20	chr6:31004800-31006000	Flanking Active TSS	NHDF-Ad	bronchial
21	chr6:31004800-31007600	Enhancers	Gastric	stomach
22	chr6:31005000-31005200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:31005000-31005200	Enhancers	Right Atrium	heart
24	chr6:31005000-31005200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr6:31005000-31005400	Flanking Active TSS	HSMM	muscle
26	chr6:31005000-31005400	Flanking Active TSS	HSMMtube	muscle
27	chr6:31005000-31005600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:31005000-31005800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr6:31005000-31005800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:31005000-31005800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:31005000-31006000	Enhancers	Brain Inferior Temporal Lobe	brain

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