Variant report

Variant	rs1476386
Chromosome Location	chr6:109764404-109764405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:109763879-109764525	HepG2	liver:	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	chr6:109763223-109764494	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr6:109763687-109764438	GM12891	blood:	n/a	n/a
9	POLR2A	chr6:109761298-109765076	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr6:109763895-109765029	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr6:109763890-109764485	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	chr6:109763203-109764429	GM12892	blood:	n/a	n/a
16	POLR2A	chr6:109761656-109772338	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:109761808-109772355	GM12891	blood:	n/a	n/a
18	POLR2A	chr6:109763255-109772269	K562	blood:	n/a	n/a
19	POLR2A	chr6:109763626-109764421	H1-neurons	neurons:	n/a	n/a
20	POLR2A	chr6:109763205-109765322	GM18505	blood:	n/a	n/a
21	POLR2A	chr6:109764140-109764491	K562	blood:	n/a	n/a
22	POLR2A	chr6:109761608-109765621	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:109699708..109703613-chr6:109762807..109765058,4	K562	blood:
2	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: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10080925	0.85[CEU][hapmap]
rs13437492	0.87[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap]
rs17070590	0.87[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17602109	0.86[EUR][1000 genomes]
rs1998813	1.00[CEU][hapmap]
rs2232441	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2275649	1.00[CEU][hapmap]
rs28635303	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3757232	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757236	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757237	0.85[JPT][hapmap];0.82[TSI][hapmap]
rs4313033	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4946969	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4946972	0.87[CEU][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap]
rs4946975	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs4946977	0.87[CEU][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap]
rs4946979	0.95[EUR][1000 genomes]
rs749621	0.87[CEU][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs9480935	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9480937	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9480938	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9480954	0.92[AFR][1000 genomes]
rs9480959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480962	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9480965	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9487071	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487077	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487078	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487083	0.92[MEX][hapmap];0.90[TSI][hapmap]
rs9487106	0.89[AFR][1000 genomes]
rs9487119	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9487124	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1476386	RP11-425D10.10	cis	Thyroid	GTEx

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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