Variant report

Variant	rs6821350
Chromosome Location	chr4:119613045-119613046
allele	G/T
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	ARID3A	chr4:119612982-119613173	K562	blood:	n/a	n/a

Variant related genes	Relation type
METTL14	TF binding region

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10022024	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11724866	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11730728	0.88[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs11735989	0.87[EUR][1000 genomes]
rs11945703	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12640223	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12646268	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12646298	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12648682	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12648778	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13105145	0.83[EUR][1000 genomes]
rs13105732	0.82[EUR][1000 genomes]
rs13111664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13115157	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13124091	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13146440	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13146816	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13150663	0.87[EUR][1000 genomes]
rs2029399	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2046779	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2288307	0.82[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs3087958	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34091082	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34270389	0.85[EUR][1000 genomes]
rs34508500	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34628947	0.85[EUR][1000 genomes]
rs35023705	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35071348	0.85[EUR][1000 genomes]
rs35392662	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35404779	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35522890	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35613641	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35952841	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36023173	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733517	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66500248	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66942289	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67151421	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67989872	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6813357	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814447	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817790	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6818241	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6827740	0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs6828070	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6829010	0.85[EUR][1000 genomes]
rs6831197	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6836005	0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837652	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6847706	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]
rs6849714	0.82[EUR][1000 genomes]
rs6852706	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6853722	0.87[EUR][1000 genomes]
rs6855919	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6857285	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71610228	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72679004	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72679023	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7653962	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7656990	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs7662650	0.84[EUR][1000 genomes]
rs7669896	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs7670182	0.85[TSI][hapmap]
rs7681835	0.86[EUR][1000 genomes]
rs7692721	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7695602	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7696543	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6821350	KIAA1627	cis	multi-tissue	Pritchard
rs6821350	METTL14	cis	lymphoblastoid	seeQTL
rs6821350	RP11-384K6.6	cis	Artery Tibial	GTEx
rs6821350	C4orf31	cis	cerebellum	SCAN
rs6821350	FGF2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119607000-119644800	Weak transcription	Small Intestine	intestine
2	chr4:119607200-119615800	Weak transcription	Esophagus	oesophagus
3	chr4:119607200-119659200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:119607400-119613200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:119607600-119615800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:119607800-119613200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:119607800-119615800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:119607800-119615800	Weak transcription	Psoas Muscle	Psoas
9	chr4:119607800-119618000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:119607800-119625600	Weak transcription	Aorta	Aorta
11	chr4:119607800-119693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:119608000-119618800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:119608000-119645000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:119608400-119613200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:119608400-119613600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:119608400-119613600	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:119608400-119613800	Weak transcription	Brain Germinal Matrix	brain
18	chr4:119608400-119615600	Weak transcription	A549	lung
19	chr4:119608400-119615800	Weak transcription	NHLF	lung
20	chr4:119608400-119618600	Weak transcription	Brain Substantia Nigra	brain
21	chr4:119608600-119618400	Weak transcription	Colonic Mucosa	Colon
22	chr4:119608600-119635200	Strong transcription	Fetal Thymus	thymus
23	chr4:119608600-119635800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:119608600-119674000	Weak transcription	Stomach Mucosa	stomach
25	chr4:119608800-119613200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:119608800-119613200	Weak transcription	GM12878-XiMat	blood
27	chr4:119608800-119613600	Weak transcription	Brain Angular Gyrus	brain
28	chr4:119608800-119613800	Weak transcription	HMEC	breast
29	chr4:119608800-119618000	Weak transcription	Hela-S3	cervix
30	chr4:119608800-119625400	Weak transcription	HSMMtube	muscle
31	chr4:119608800-119635000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr4:119609000-119614600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:119609000-119614600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:119609000-119615600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr4:119609000-119620000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:119609000-119620400	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr4:119609000-119620800	Strong transcription	Liver	Liver
38	chr4:119609000-119621200	Strong transcription	Osteobl	bone
39	chr4:119609000-119622600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr4:119609000-119628200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:119609000-119633200	Strong transcription	Placenta	Placenta
42	chr4:119609000-119633400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:119609000-119633400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:119609000-119633800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:119609000-119634400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:119609000-119634800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr4:119609000-119635000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:119609000-119635000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr4:119609000-119636000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:119609000-119636200	Strong transcription	Monocytes-CD14+_RO01746	blood

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