Variant report

Variant	rs2046779
Chromosome Location	chr4:119653822-119653823
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	chr4:119653579-119654400	K562	blood:	n/a	n/a
2	GATA1	chr4:119653744-119655005	PBDE	blood:	n/a	n/a
3	POLR2A	chr4:119653684-119654507	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119653222..119655642-chr4:119658116..119660847,2	K562	blood:

Variant related genes	Relation type
SEC24D	TF binding region
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10022024	0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs11724866	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11730728	0.95[CEU][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs11735989	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs11945703	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12640223	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12646268	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12646298	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12648682	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12648778	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13105145	0.84[EUR][1000 genomes]
rs13105732	0.83[EUR][1000 genomes]
rs13111664	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13115157	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13124091	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13146440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13146816	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13150663	0.89[EUR][1000 genomes]
rs2029399	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288307	0.95[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs3087958	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34091082	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34270389	0.86[EUR][1000 genomes]
rs34508500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34628947	0.86[EUR][1000 genomes]
rs35023705	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35071348	0.88[EUR][1000 genomes]
rs35392662	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35404779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35522890	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[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];0.91[ASN][1000 genomes]
rs36023173	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733517	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.91[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]
rs66500248	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66942289	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67151421	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67989872	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6813357	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6814447	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6817790	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6818241	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6821350	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]
rs6827740	0.95[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs6828070	0.85[ASN][1000 genomes]
rs6829010	0.88[EUR][1000 genomes]
rs6831197	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6836005	0.88[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6836261	0.82[YRI][hapmap]
rs6837652	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6847706	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]
rs6849714	0.83[EUR][1000 genomes]
rs6852706	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6853722	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs6855919	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6857285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71610228	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72679004	0.82[AMR][1000 genomes]
rs72679023	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7653962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7656990	0.94[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap]
rs7662650	0.86[EUR][1000 genomes]
rs7669896	0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap]
rs7670182	0.86[CEU][hapmap];0.87[TSI][hapmap]
rs7681835	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs7692721	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.91[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]
rs7695602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7696543	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2046779	RP11-384K6.6	cis	Artery Tibial	GTEx
rs2046779	KIAA1627	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119607200-119659200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:119607800-119693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:119608600-119674000	Weak transcription	Stomach Mucosa	stomach
4	chr4:119620000-119660200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:119625800-119718000	Weak transcription	Hela-S3	cervix
6	chr4:119628000-119659800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:119628400-119657600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr4:119630400-119674200	Weak transcription	A549	lung
9	chr4:119633200-119662800	Weak transcription	Brain Anterior Caudate	brain
10	chr4:119633400-119667600	Weak transcription	Brain Germinal Matrix	brain
11	chr4:119634400-119660000	Weak transcription	Brain Angular Gyrus	brain
12	chr4:119640600-119662200	Strong transcription	Fetal Muscle Trunk	muscle
13	chr4:119640800-119692600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr4:119641200-119659600	Strong transcription	Fetal Intestine Large	intestine
15	chr4:119641600-119659400	Strong transcription	Liver	Liver
16	chr4:119641600-119679800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr4:119642000-119654400	Strong transcription	Stomach Smooth Muscle	stomach
18	chr4:119642000-119661200	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr4:119642000-119662000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:119642000-119662000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr4:119642000-119666800	Strong transcription	Placenta	Placenta
22	chr4:119642200-119668200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr4:119642400-119656400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr4:119642400-119662000	Strong transcription	Adipose Nuclei	Adipose
25	chr4:119642400-119662000	Strong transcription	Fetal Lung	lung
26	chr4:119642400-119668400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:119643000-119658400	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr4:119643000-119662000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:119644200-119659600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:119644400-119655000	Strong transcription	Dnd41	blood
31	chr4:119644400-119662000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:119644400-119662000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr4:119644400-119667400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:119644600-119654400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:119644800-119654400	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:119645400-119654000	Strong transcription	Rectal Smooth Muscle	rectum
37	chr4:119645400-119668200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:119645800-119654400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:119645800-119654400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr4:119646000-119654400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:119646000-119654400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:119646200-119657800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:119646200-119662200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:119646200-119667000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:119646600-119662000	Strong transcription	GM12878-XiMat	blood
46	chr4:119647000-119654400	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr4:119647400-119660400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr4:119648800-119656400	Weak transcription	Colonic Mucosa	Colon
49	chr4:119649200-119659200	Weak transcription	Right Ventricle	heart
50	chr4:119649200-119665200	Weak transcription	Small Intestine	intestine

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