Variant report

Variant	rs6847706
Chromosome Location	chr4:119661552-119661553
allele	C/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	POLR2A	chr4:119661536-119661626	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
SEC24D	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10022024	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap]
rs11724866	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11730728	0.95[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs11735989	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs11945703	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12640223	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12646268	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12646298	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12648682	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12648778	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13105145	0.85[EUR][1000 genomes]
rs13105732	0.83[EUR][1000 genomes]
rs13111664	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13115157	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13124091	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13146440	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13146816	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13150663	0.90[EUR][1000 genomes]
rs2029399	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2046779	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288307	0.95[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs3087958	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34091082	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34270389	0.86[EUR][1000 genomes]
rs34508500	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34628947	0.86[EUR][1000 genomes]
rs35023705	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35071348	0.88[EUR][1000 genomes]
rs35392662	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35404779	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35522890	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35613641	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35952841	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36023173	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3733517	0.89[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66500248	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66942289	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67151421	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67989872	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6813357	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6814447	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6817790	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6818241	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6821350	0.89[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6827740	0.95[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs6828070	0.83[ASN][1000 genomes]
rs6829010	0.88[EUR][1000 genomes]
rs6831197	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6836005	0.88[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6837652	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6849714	0.84[EUR][1000 genomes]
rs6852706	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6853722	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6855919	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6857285	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71610228	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72679004	0.82[AMR][1000 genomes]
rs72679023	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7653962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7656990	0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs7662650	0.87[EUR][1000 genomes]
rs7669896	0.94[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap]
rs7670182	0.86[CEU][hapmap];0.88[TSI][hapmap]
rs7681835	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs7692721	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7695602	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7696543	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS 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	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv427693	chr4:119493919-119674742	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6847706	METTL14	cis	lymphoblastoid	seeQTL
rs6847706	FGF2	cis	parietal	SCAN
rs6847706	RP11-384K6.6	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119607800-119693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:119608600-119674000	Weak transcription	Stomach Mucosa	stomach
3	chr4:119625800-119718000	Weak transcription	Hela-S3	cervix
4	chr4:119630400-119674200	Weak transcription	A549	lung
5	chr4:119633200-119662800	Weak transcription	Brain Anterior Caudate	brain
6	chr4:119633400-119667600	Weak transcription	Brain Germinal Matrix	brain
7	chr4:119640600-119662200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr4:119640800-119692600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:119641600-119679800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr4:119642000-119662000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:119642000-119662000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr4:119642000-119666800	Strong transcription	Placenta	Placenta
13	chr4:119642200-119668200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:119642400-119662000	Strong transcription	Adipose Nuclei	Adipose
15	chr4:119642400-119662000	Strong transcription	Fetal Lung	lung
16	chr4:119642400-119668400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:119643000-119662000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:119644400-119662000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr4:119644400-119662000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:119644400-119667400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:119645400-119668200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:119646200-119662200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:119646200-119667000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:119646600-119662000	Strong transcription	GM12878-XiMat	blood
25	chr4:119649200-119665200	Weak transcription	Small Intestine	intestine
26	chr4:119649200-119666800	Weak transcription	Psoas Muscle	Psoas
27	chr4:119649200-119670600	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:119649200-119675200	Weak transcription	Brain Substantia Nigra	brain
29	chr4:119649200-119687600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:119649200-119693600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:119649600-119664600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr4:119650600-119668400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:119651400-119664600	Weak transcription	Fetal Brain Male	brain
34	chr4:119651800-119665400	Strong transcription	HUVEC	blood vessel
35	chr4:119651800-119672600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr4:119651800-119687400	Weak transcription	Thymus	Thymus
37	chr4:119652000-119661600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr4:119652000-119672400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr4:119653200-119663800	Weak transcription	Esophagus	oesophagus
40	chr4:119653400-119668400	Strong transcription	HepG2	liver
41	chr4:119654200-119662400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr4:119654400-119662400	Weak transcription	Fetal Heart	heart
43	chr4:119654400-119662600	Weak transcription	Gastric	stomach
44	chr4:119654400-119666200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:119654400-119672600	Strong transcription	NH-A	brain
46	chr4:119654400-119687400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr4:119654800-119676000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:119655200-119661800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:119655200-119662400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:119655200-119662600	Strong transcription	Osteobl	bone

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