Variant report

Variant	rs6747862
Chromosome Location	chr2:127965845-127965846
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr2:127965833-127966204	ECC-1	luminal epithelium:	n/a	n/a
2	TEAD4	chr2:127965783-127966282	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr2:127965769-127966308	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr2:127965845-127966232	H1-hESC	embryonic stem cell:	n/a	n/a
5	TCF12	chr2:127965733-127966403	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:127965809..127968370-chr2:127982231..127984174,2	K562	blood:

Variant related genes	Relation type
CYP27C1	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs10167294	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10928764	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs1143407	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11684068	0.95[CEU][hapmap]
rs11899601	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12613252	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12613254	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12613413	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs12614320	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12617858	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12619391	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13017103	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13390029	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13403918	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13409933	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13414676	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13429925	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2134794	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2276682	0.95[CEU][hapmap]
rs28807127	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34441363	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34487399	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34601617	0.90[EUR][1000 genomes]
rs34703177	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738948	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3893313	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4150434	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs4150492	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4150506	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4150514	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4300780	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4359587	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4528711	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4662721	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4662724	0.95[CEU][hapmap]
rs58063879	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59027829	0.84[EUR][1000 genomes]
rs6430937	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6716392	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6735779	0.95[CEU][hapmap]
rs6738811	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6752139	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9752366	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9923	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv961678	chr2:127961305-127979990	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv3331416	chr2:127962771-127980988	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs6747862	AC068282.3	cis	Esophagus Mucosa	GTEx
rs6747862	AC068282.3	cis	lung	GTEx
rs6747862	AC068282.3	cis	Muscle Skeletal	GTEx
rs6747862	MAP3K2	cis	Frontal Cortex	GTEx
rs6747862	MAP3K2	cis	Brain Pons	GTEx
rs6747862	AC068282.3	cis	Thyroid	GTEx
rs6747862	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6747862	MAP3K2	cis	multi-tissue	Pritchard
rs6747862	AC068282.3	cis	Heart Left Ventricle	GTEx
rs6747862	AC068282.3	cis	Artery Aorta	GTEx
rs6747862	AC068282.3	cis	Artery Tibial	GTEx
rs6747862	AC068282.3	cis	Whole Blood	GTEx
rs6747862	MAP3K2	cis	Cerebellum	GTEx
rs6747862	MAP3K2	cis	Temporal Cortex	GTEx
rs6747862	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs6747862	AC068282.3	cis	Esophagus Muscularis	GTEx
rs6747862	AC068282.3	cis	Nerve Tibial	GTEx
rs6747862	AC068282.3	cis	Stomach	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127948800-127973400	Weak transcription	HMEC	breast
2	chr2:127952200-127975200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:127956400-127975800	Weak transcription	Fetal Kidney	kidney
4	chr2:127965400-127967000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr2:127965600-127966000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:127965600-127966000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr2:127965600-127966000	ZNF genes & repeats	Fetal Muscle Leg	muscle
8	chr2:127965600-127966400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr2:127965600-127966400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr2:127965600-127966600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr2:127965600-127966600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:127965600-127966600	Enhancers	Hela-S3	cervix
13	chr2:127965600-127966600	Enhancers	HSMM	muscle
14	chr2:127965600-127966800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr2:127965600-127966800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:127965600-127966800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:127965600-127967000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:127965600-127967200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:127965800-127966000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr2:127965800-127966000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
21	chr2:127965800-127966000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr2:127965800-127966000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr2:127965800-127966200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:127965800-127966200	Enhancers	Fetal Lung	lung
25	chr2:127965800-127966400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr2:127965800-127966400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:127965800-127966400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:127965800-127966400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:127965800-127966600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:127965800-127966600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:127965800-127966600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:127965800-127966600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:127965800-127966600	Enhancers	NHEK	skin
34	chr2:127965800-127966800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:127965800-127966800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:127965800-127966800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:127965800-127966800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:127965800-127966800	Enhancers	H9 Cell Line	embryonic stem cell
39	chr2:127965800-127966800	Enhancers	Esophagus	oesophagus
40	chr2:127965800-127966800	Enhancers	Placenta	Placenta
41	chr2:127965800-127967200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:127965800-127967200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:127965800-127967400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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