Variant report

Variant	rs11078342
Chromosome Location	chr17:16353617-16353618
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:16341231-16355258	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr17:16353399-16353624	MCF10A-Er-Src	breast:	n/a	n/a
3	BCL3	chr17:16353204-16353619	A549	lung:	n/a	n/a
4	POLR2A	chr17:16353181-16354530	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr17:16353598-16353634	ProgFib	skin:	n/a	n/a
6	POLR2A	chr17:16353129-16354727	HCT-116	colon:	n/a	n/a
7	POLR2A	chr17:16353077-16354688	U87	brain:	n/a	n/a
8	POLR2A	chr17:16353538-16354490	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr17:16353281-16354641	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr17:16353252-16353638	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr17:16353354-16353681	SK-N-SH	brain:	n/a	n/a
12	BCL3	chr17:16353289-16354794	A549	lung:	n/a	n/a
13	POLR2A	chr17:16353077-16354639	U87	brain:	n/a	n/a
14	POLR2A	chr17:16353291-16354607	A549	lung:	n/a	n/a
15	POLR2A	chr17:16353146-16354728	U87	brain:	n/a	n/a
16	POLR2A	chr17:16353453-16354680	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr17:16353211-16354114	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr17:16353145-16354284	A549	lung:	n/a	n/a
19	POLR2A	chr17:16353190-16354715	MCF-7	breast:	n/a	n/a
20	POLR2A	chr17:16353248-16354285	HepG2	liver:	n/a	n/a
21	JUND	chr17:16353288-16353883	A549	lung:	n/a	n/a
22	POLR2A	chr17:16353089-16354889	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr17:16353520-16353686	GM12878	blood:	n/a	n/a
24	POLR2A	chr17:16353307-16353673	K562	blood:	n/a	n/a
25	POLR2A	chr17:16353146-16354729	K562	blood:	n/a	n/a
26	POLR2A	chr17:16353164-16354728	U87	brain:	n/a	n/a
27	POLR2A	chr17:16353266-16354071	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr17:16353273-16354514	HepG2	liver:	n/a	n/a
29	POLR2A	chr17:16353266-16353778	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr17:16353220-16354745	K562	blood:	n/a	n/a
31	POLR2A	chr17:16341165-16355366	HepG2	liver:	n/a	n/a
32	POLR2A	chr17:16341299-16354759	K562	blood:	n/a	n/a
33	POLR2A	chr17:16353511-16353685	A549	lung:	n/a	n/a
34	POLR2A	chr17:16353212-16354648	HepG2	liver:	n/a	n/a
35	POLR2A	chr17:16353248-16354660	HepG2	liver:	n/a	n/a
36	POLR2A	chr17:16353184-16354456	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr17:16353609-16354662	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr17:16353362-16354769	HCT-116	colon:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16282285..16286163-chr17:16348924..16355139,5	K562	blood:

No data

Variant related genes	Relation type
FAM211A	TF binding region
ENSG00000170315	Chromatin interaction
ENSG00000265401	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1029809	1.00[JPT][hapmap]
rs11078343	1.00[CEU][hapmap];1.00[JPT][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]
rs11078344	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11078345	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11650427	1.00[JPT][hapmap]
rs11653149	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11654069	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11867498	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11869614	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11870279	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871017	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871929	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871958	0.91[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11871963	1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936240	0.84[AMR][1000 genomes]
rs12938294	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12940078	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17552310	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17715447	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34166276	0.84[AMR][1000 genomes]
rs34192401	0.84[AMR][1000 genomes]
rs34419652	0.84[AMR][1000 genomes]
rs34572942	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34577506	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34779276	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34793697	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34982046	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35034622	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35247166	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35269706	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35377488	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35474528	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35540454	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35774281	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36117589	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56097826	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217211	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941411	0.95[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
6	nsv1061463	chr17:16245878-16490691	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
7	nsv543216	chr17:16245878-16490691	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
8	nsv1065254	chr17:16252880-16389930	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
9	nsv428668	chr17:16265210-16455285	Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11078342	C17orf45	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16343800-16354600	Strong transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:16343800-16363400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:16344600-16372800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr17:16344800-16355000	Strong transcription	Fetal Stomach	stomach
5	chr17:16345000-16354600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:16345200-16354600	Strong transcription	Thymus	Thymus
7	chr17:16345800-16363200	Weak transcription	Small Intestine	intestine
8	chr17:16345800-16373200	Weak transcription	Psoas Muscle	Psoas
9	chr17:16346000-16354600	Strong transcription	Primary T cells from cord blood	blood
10	chr17:16346400-16354200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr17:16346400-16362400	Weak transcription	Hela-S3	cervix
12	chr17:16346400-16362600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr17:16346400-16363800	Weak transcription	Fetal Kidney	kidney
14	chr17:16347000-16356800	Weak transcription	HSMMtube	muscle
15	chr17:16347000-16363000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr17:16347000-16366400	Weak transcription	NHDF-Ad	bronchial
17	chr17:16347400-16356400	Weak transcription	Fetal Brain Male	brain
18	chr17:16347600-16354600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:16347800-16367000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr17:16348000-16354800	Strong transcription	Dnd41	blood
21	chr17:16348000-16356600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr17:16348200-16354200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr17:16348200-16354600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr17:16348600-16354600	Strong transcription	Gastric	stomach
25	chr17:16349000-16354600	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr17:16349000-16354600	Strong transcription	Fetal Brain Female	brain
27	chr17:16349000-16355800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr17:16349000-16366600	Weak transcription	Right Atrium	heart
29	chr17:16349200-16354600	Strong transcription	Brain Germinal Matrix	brain
30	chr17:16349200-16354600	Strong transcription	Fetal Intestine Large	intestine
31	chr17:16349200-16354600	Strong transcription	Fetal Thymus	thymus
32	chr17:16349200-16363200	Weak transcription	Stomach Mucosa	stomach
33	chr17:16349600-16354400	Strong transcription	Colonic Mucosa	Colon
34	chr17:16349600-16354600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr17:16349600-16356800	Strong transcription	Fetal Intestine Small	intestine
36	chr17:16349800-16356600	Weak transcription	Fetal Heart	heart
37	chr17:16350000-16366600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr17:16350200-16354600	Strong transcription	Fetal Muscle Leg	muscle
39	chr17:16350200-16366600	Weak transcription	Fetal Lung	lung
40	chr17:16350600-16354600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr17:16350600-16354800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr17:16351000-16354000	Strong transcription	K562	blood
43	chr17:16351200-16354600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr17:16351400-16353800	Strong transcription	A549	lung
45	chr17:16351400-16354800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr17:16351400-16363000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr17:16351600-16354600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr17:16351600-16354600	Strong transcription	Fetal Muscle Trunk	muscle
49	chr17:16351800-16354600	Strong transcription	Brain Angular Gyrus	brain
50	chr17:16352000-16354400	Strong transcription	Esophagus	oesophagus

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