Variant report

Variant	rs12981023
Chromosome Location	chr19:44008489-44008490
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:43997566..43999974-chr19:44006795..44009700,2	K562	blood:
2	chr19:43997566..43999110-chr19:44006795..44008578,2	K562	blood:
3	chr19:43967204..43969877-chr19:44006593..44010322,9	MCF-7	breast:
4	chr19:43966113..43971089-chr19:44005040..44010546,6	K562	blood:
5	chr19:44007568..44009583-chr19:44036201..44039639,3	MCF-7	breast:
6	chr19:43965066..43971111-chr19:44006791..44009897,14	MCF-7	breast:
7	chr19:44006689..44009864-chr19:44027261..44031051,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176472	Chromatin interaction
ENSG00000176531	Chromatin interaction
ENSG00000124466	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12460021	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12973764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12979907	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12980646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184239	0.88[CEU][hapmap]
rs2102954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs2682585	0.89[CEU][hapmap]
rs2682586	0.88[CEU][hapmap]
rs2854506	0.83[CEU][hapmap]
rs2854508	0.83[CEU][hapmap]
rs2854509	0.83[CEU][hapmap]
rs304731	0.87[CEU][hapmap];0.92[YRI][hapmap]
rs34977009	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35016410	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35485252	0.86[EUR][1000 genomes]
rs36034157	0.80[EUR][1000 genomes]
rs36075334	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3810381	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4507015	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4544340	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4802183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59000923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59827264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61607741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509094	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71362654	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7248167	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7248927	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7252962	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7253177	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7253856	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs762506	0.83[CEU][hapmap]
rs8100211	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	esv2762041	chr19:43986023-44014457	Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12981023	ETHE1	Cis_1M	lymphoblastoid	RTeQTL
rs12981023	ETHE1	cis	multi-tissue	Pritchard
rs12981023	LOC653583///PHLDB3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44006200-44008600	Active TSS	Colonic Mucosa	Colon
2	chr19:44006600-44008800	Active TSS	Fetal Brain Female	brain
3	chr19:44007000-44009000	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr19:44007000-44009200	Active TSS	Esophagus	oesophagus
5	chr19:44007000-44009200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr19:44007200-44009000	Active TSS	Brain Anterior Caudate	brain
7	chr19:44007200-44009200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:44007200-44009200	Active TSS	Rectal Smooth Muscle	rectum
9	chr19:44007200-44009400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr19:44007400-44008600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:44007400-44008600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:44007400-44008800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:44007400-44008800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr19:44007400-44008800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:44007400-44008800	Active TSS	HSMM	muscle
16	chr19:44007400-44008800	Active TSS	NHLF	lung
17	chr19:44007400-44009000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:44007400-44009000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:44007400-44009000	Active TSS	Fetal Kidney	kidney
20	chr19:44007400-44009000	Active TSS	GM12878-XiMat	blood
21	chr19:44007400-44009200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:44007400-44009200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr19:44007400-44009400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:44007400-44009400	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr19:44007600-44008600	Bivalent/Poised TSS	Fetal Stomach	stomach
26	chr19:44007600-44008600	Active TSS	HUVEC	blood vessel
27	chr19:44007600-44008800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:44007600-44008800	Active TSS	Primary T cells from cord blood	blood
29	chr19:44007600-44008800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:44007600-44008800	Bivalent/Poised TSS	HepG2	liver
31	chr19:44007600-44008800	Active TSS	HSMMtube	muscle
32	chr19:44007600-44008800	Active TSS	Osteobl	bone
33	chr19:44007600-44009000	Active TSS	Brain Hippocampus Middle	brain
34	chr19:44007600-44009000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:44007600-44009000	Active TSS	Fetal Intestine Small	intestine
36	chr19:44007600-44009000	Active TSS	Left Ventricle	heart
37	chr19:44007600-44009000	Active TSS	Psoas Muscle	Psoas
38	chr19:44007600-44009200	Active TSS	Aorta	Aorta
39	chr19:44007600-44009200	Active TSS	Brain Angular Gyrus	brain
40	chr19:44007600-44009200	Active TSS	Fetal Intestine Large	intestine
41	chr19:44007600-44009200	Active TSS	Ovary	ovary
42	chr19:44007600-44009200	Active TSS	Pancreas	Pancrea
43	chr19:44007600-44009200	Active TSS	Right Atrium	heart
44	chr19:44007600-44009400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
45	chr19:44007600-44009400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr19:44007600-44009400	Active TSS	NHDF-Ad	bronchial
47	chr19:44007800-44008600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:44007800-44008600	Active TSS	Liver	Liver
49	chr19:44007800-44008600	Active TSS	Stomach Smooth Muscle	stomach
50	chr19:44007800-44008800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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