Variant report

Variant	rs1476387
Chromosome Location	chr6:109764535-109764536
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:109764520-109765073	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:109763078-109765366	GM12892	blood:	n/a	n/a
3	POLR2A	chr6:109763136-109764996	GM12891	blood:	n/a	n/a
4	POLR2A	chr6:109763235-109765443	GM19193	blood:	n/a	n/a
5	POLR2A	chr6:109762774-109764553	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr6:109761754-109765661	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:109764530-109764564	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:109761298-109765076	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:109764528-109764544	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:109763895-109765029	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr6:109764484-109764977	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:109763209-109771395	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr6:109761500-109772072	GM12892	blood:	n/a	n/a
14	POLR2A	chr6:109763115-109765540	GM12892	blood:	n/a	n/a
15	POLR2A	chr6:109761656-109772338	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:109761808-109772355	GM12891	blood:	n/a	n/a
17	POLR2A	chr6:109763255-109772269	K562	blood:	n/a	n/a
18	POLR2A	chr6:109763205-109765322	GM18505	blood:	n/a	n/a
19	POLR2A	chr6:109761608-109765621	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109764530..109766922-chr6:109796354..109798276,2	K562	blood:
2	chr6:109699708..109703613-chr6:109762807..109765058,4	K562	blood:
3	chr6:109702065..109705528-chr6:109760483..109765471,8	MCF-7	breast:

No data

Variant related genes	Relation type
PPIL6	TF binding region
ENSG00000135535	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10457192	0.88[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap]
rs10457194	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs10457195	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs1046943	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1054607	0.82[JPT][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap]
rs1074765	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1074766	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10872033	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11153171	0.87[CHB][hapmap]
rs11153183	0.88[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs11251	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11754455	0.87[CEU][hapmap];0.89[JPT][hapmap]
rs11755641	0.88[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs12194061	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs12197180	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs12198938	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs12199154	0.88[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs12212476	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs12214147	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12529733	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs13201430	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs13219952	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13220915	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs1406899	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs1521907	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17070591	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17070656	0.80[YRI][hapmap]
rs1853330	0.85[EUR][1000 genomes]
rs1885690	0.93[EUR][1000 genomes]
rs1885691	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1980591	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs1998811	0.80[EUR][1000 genomes]
rs2024850	0.88[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap]
rs2024853	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs2211288	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2236084	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2277113	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2277114	0.88[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs2884037	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs35146243	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35260632	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3734652	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3757230	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3757231	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3757235	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3778474	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3778478	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3799842	0.85[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3818933	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4636056	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4945831	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946967	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4946970	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4946976	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58644322	0.93[EUR][1000 genomes]
rs59597139	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6568587	0.80[YRI][hapmap]
rs6911838	0.84[CHB][hapmap]
rs6914216	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6920372	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6920712	0.82[JPT][hapmap];0.84[MKK][hapmap];0.85[YRI][hapmap]
rs6925005	0.80[YRI][hapmap]
rs6939548	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6939953	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs699700	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs729888	0.88[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs730089	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs736830	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs746794	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7748669	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7751582	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7754650	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755941	0.87[CEU][hapmap];0.85[GIH][hapmap]
rs7768973	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7773950	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs8465	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs910730	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9320286	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9372213	0.81[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9398202	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9480947	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9480949	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9480956	1.00[CEU][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9480958	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487064	0.88[EUR][1000 genomes]
rs9487066	0.86[EUR][1000 genomes]
rs9487069	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9487070	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9487076	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9487084	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9487085	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9487103	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs974034	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9791241	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1476387	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs1476387	SMPD2	cis	parietal	SCAN
rs1476387	FIG4	cis	cerebellum	SCAN
rs1476387	MICAL1	cis	Artery Tibial	GTEx
rs1476387	ZBTB24	cis	cerebellum	SCAN
rs1476387	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs1476387	CD164	cis	parietal	SCAN
rs1476387	AKD1	cis	cerebellum	SCAN
rs1476387	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs1476387	SMPD2	cis	Esophagus Mucosa	GTEx
rs1476387	RP11-425D10.10	cis	Whole Blood	GTEx
rs1476387	FIG4	cis	parietal	SCAN
rs1476387	AKD1	cis	parietal	SCAN
rs1476387	SMPD2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109762800-109775800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:109763000-109764600	Weak transcription	Aorta	Aorta
3	chr6:109763000-109765000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:109763000-109765600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:109763200-109764600	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr6:109763200-109764600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr6:109763200-109765000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:109763200-109765000	Genic enhancers	Pancreas	Pancrea
9	chr6:109763200-109765400	Weak transcription	A549	lung
10	chr6:109763200-109765400	Weak transcription	NHDF-Ad	bronchial
11	chr6:109763200-109765400	Weak transcription	Osteobl	bone
12	chr6:109763200-109774400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:109763200-109775600	Weak transcription	Fetal Kidney	kidney
14	chr6:109763200-109775800	Weak transcription	HUVEC	blood vessel
15	chr6:109763400-109764600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:109763400-109764600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr6:109763400-109765000	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:109763400-109765000	Weak transcription	HSMMtube	muscle
19	chr6:109763400-109765200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:109763400-109765400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr6:109763400-109765800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr6:109763400-109766000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:109763400-109766200	Genic enhancers	Esophagus	oesophagus
24	chr6:109763400-109766400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr6:109763400-109768600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:109763400-109770400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:109763400-109775000	Strong transcription	NHLF	lung
28	chr6:109763400-109775200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:109763600-109764600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:109763600-109764800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:109763600-109764800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr6:109763600-109764800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr6:109763600-109764800	Genic enhancers	Lung	lung
34	chr6:109763600-109765000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr6:109763600-109765000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:109763600-109765000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr6:109763600-109765200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:109763600-109765400	Weak transcription	NH-A	brain
39	chr6:109763600-109765600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:109763600-109765600	Weak transcription	Ovary	ovary
41	chr6:109763600-109766000	Weak transcription	Brain Angular Gyrus	brain
42	chr6:109763600-109767400	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:109763600-109768200	Strong transcription	Fetal Lung	lung
44	chr6:109763600-109768400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:109763600-109768400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:109763600-109768400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr6:109763600-109768400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:109763600-109768600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr6:109763600-109768600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:109763600-109768800	Strong transcription	H1 Cell Line	embryonic stem cell

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