Variant report

Variant	rs17234092
Chromosome Location	chr3:53265581-53265582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:53265566-53266113	A549	lung:	n/a	n/a
2	POLR2A	chr3:53263211-53265592	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr3:53264736-53267552	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:53265100-53267084	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:53260293-53267557	HL-60	blood:	n/a	n/a
6	POLR2A	chr3:53264951-53265725	K562	blood:	n/a	n/a
7	POLR2A	chr3:53263775-53266066	GM12891	blood:	n/a	n/a
8	POLR2A	chr3:53264809-53266611	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:53261891-53271225	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:53263518-53266795	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:53261830-53267534	GM12892	blood:	n/a	n/a
12	POLR2A	chr3:53265546-53266137	A549	lung:	n/a	n/a
13	POLR2A	chr3:53264706-53269099	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:53261940-53270977	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:53265199-53265582	HCT-116	colon:	n/a	n/a
16	POLR2A	chr3:53265222-53265895	K562	blood:	n/a	n/a
17	POLR2A	chr3:53264872-53267077	K562	blood:	n/a	n/a
18	POLR2A	chr3:53261824-53267608	GM12892	blood:	n/a	n/a
19	POLR2A	chr3:53261936-53267421	K562	blood:	n/a	n/a
20	POLR2A	chr3:53264000-53267356	GM18505	blood:	n/a	n/a
21	POLR2A	chr3:53265557-53266180	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:53264807-53269247	HL-60	blood:	n/a	n/a
23	SP1	chr3:53265258-53265648	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:53253532-53269075	A549	lung:	n/a	n/a
25	POLR2A	chr3:53265567-53267348	NB4	blood:	n/a	n/a
26	POLR2A	chr3:53255471-53271280	K562	blood:	n/a	n/a
27	POLR2A	chr3:53265574-53266341	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr3:53264694-53267466	HEK293	kidney:	n/a	n/a
29	POLR2A	chr3:53265553-53267439	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:53261843-53267417	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:53264921-53267474	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:53263303-53267449	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr3:53265303-53265922	MCF-7	breast:	n/a	n/a
34	POLR2A	chr3:53265499-53266575	HCT-116	colon:	n/a	n/a
35	POLR2A	chr3:53265572-53267352	GM12891	blood:	n/a	n/a
36	POLR2A	chr3:53263612-53267450	GM12892	blood:	n/a	n/a
37	POLR2A	chr3:53265569-53266102	K562	blood:	n/a	n/a
38	POLR2A	chr3:53264886-53267316	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr3:53262196-53267537	GM12892	blood:	n/a	n/a
40	POLR2A	chr3:53264626-53267328	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53263712..53265819-chr3:53304874..53307610,2	K562	blood:

No data

Variant related genes	Relation type
TKT	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10433617	1.00[CHB][hapmap]
rs10433618	1.00[CHB][hapmap]
rs11551405	1.00[CHB][hapmap]
rs17234771	1.00[CHB][hapmap]
rs17306163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62255989	0.81[EUR][1000 genomes]
rs9826552	1.00[CHB][hapmap]
rs9830594	1.00[CHB][hapmap]
rs9850440	1.00[CHB][hapmap]
rs9864057	0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17234092	PRKCD	cis	parietal	SCAN
rs17234092	TLR9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53229000-53270000	Weak transcription	Right Atrium	heart
2	chr3:53254400-53267200	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:53254400-53270400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:53255600-53266800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:53255600-53267200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:53255600-53274400	Strong transcription	GM12878-XiMat	blood
7	chr3:53255800-53267600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr3:53255800-53269800	Genic enhancers	A549	lung
9	chr3:53255800-53269800	Strong transcription	Osteobl	bone
10	chr3:53256000-53269600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:53256000-53269600	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr3:53256000-53269600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:53256200-53267000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:53256200-53267200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr3:53256200-53269000	Strong transcription	Right Ventricle	heart
16	chr3:53256200-53269600	Strong transcription	Fetal Intestine Small	intestine
17	chr3:53256200-53269600	Strong transcription	NHLF	lung
18	chr3:53256200-53270000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:53256200-53270000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:53256200-53270000	Strong transcription	Duodenum Mucosa	Duodenum
21	chr3:53256400-53266400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:53256400-53266800	Strong transcription	Placenta	Placenta
23	chr3:53256400-53269400	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:53256400-53269600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:53256400-53270000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:53256400-53270000	Weak transcription	Fetal Kidney	kidney
27	chr3:53256400-53270000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr3:53256400-53270200	Strong transcription	Fetal Thymus	thymus
29	chr3:53256400-53272400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:53256400-53276400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:53256400-53276600	Strong transcription	Fetal Brain Female	brain
32	chr3:53256400-53276800	Strong transcription	Fetal Stomach	stomach
33	chr3:53256600-53265800	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:53256600-53268400	Strong transcription	Esophagus	oesophagus
35	chr3:53256600-53269600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:53256600-53270000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:53256600-53270000	Strong transcription	Lung	lung
38	chr3:53256600-53272000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:53256800-53269000	Strong transcription	Liver	Liver
40	chr3:53256800-53269600	Strong transcription	HMEC	breast
41	chr3:53256800-53269800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:53256800-53270000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:53256800-53270000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr3:53256800-53272200	Strong transcription	Brain Germinal Matrix	brain
45	chr3:53256800-53276600	Strong transcription	Thymus	Thymus
46	chr3:53256800-53277000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:53256800-53277000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:53257000-53266800	Strong transcription	HSMMtube	muscle
49	chr3:53257000-53269600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:53257000-53270400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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