Variant report

Variant	rs9911289
Chromosome Location	chr17:20909045-20909046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:20899351-20909849	K562	blood:	n/a	n/a
2	POLR2A	chr17:20907160-20909765	A549	lung:	n/a	n/a
3	POLR2A	chr17:20908981-20910160	HepG2	liver:	n/a	n/a
4	POLR2A	chr17:20907220-20909606	GM12878	blood:	n/a	n/a
5	POLR2A	chr17:20907153-20909554	GM12892	blood:	n/a	n/a
6	POLR2A	chr17:20907170-20909483	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr17:20908369-20909370	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr17:20907117-20909217	GM12891	blood:	n/a	n/a
9	POLR2A	chr17:20908344-20909397	K562	blood:	n/a	n/a
10	POLR2A	chr17:20908822-20909427	HL-60	blood:	n/a	n/a
11	POLR2A	chr17:20908145-20909069	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr17:20907187-20909643	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr17:20907254-20909079	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr17:20907159-20909329	GM12891	blood:	n/a	n/a
15	POLR2A	chr17:20907287-20909707	GM12878	blood:	n/a	n/a
16	POLR2A	chr17:20907229-20909082	GM12878	blood:	n/a	n/a
17	POLR2A	chr17:20907188-20909472	K562	blood:	n/a	n/a
18	POLR2A	chr17:20907161-20909791	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr17:20907224-20909513	GM12892	blood:	n/a	n/a
20	POLR2A	chr17:20907358-20909733	HepG2	liver:	n/a	n/a
21	POLR2A	chr17:20908923-20909076	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr17:20907049-20909718	GM12892	blood:	n/a	n/a
23	POLR2A	chr17:20907264-20909541	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr17:20908878-20909435	MCF-7	breast:	n/a	n/a
25	POLR2A	chr17:20908111-20909051	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr17:20908304-20909066	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr17:20908688-20909496	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr17:20907289-20909107	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	chr17:20902261..20904753-chr17:20906540..20909495,2	MCF-7	breast:
2	chr17:20907867..20912757-chr17:20913311..20916594,7	K562	blood:

No data

Variant related genes	Relation type
USP22	TF binding region
ENSG00000124422	Chromatin interaction
ENSG00000263986	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1044420	0.91[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs1045162	0.92[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1127814	0.91[ASN][1000 genomes]
rs12600703	0.89[JPT][hapmap]
rs12602058	0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12943067	0.90[ASN][1000 genomes]
rs12946114	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1531566	0.88[ASN][1000 genomes]
rs17770614	0.85[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2054464	0.88[ASN][1000 genomes]
rs2127095	0.88[ASN][1000 genomes]
rs2291034	0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2364326	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4445951	0.89[ASN][1000 genomes]
rs4985814	0.90[ASN][1000 genomes]
rs4985815	0.89[ASN][1000 genomes]
rs4985816	0.90[ASN][1000 genomes]
rs4985959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985967	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985968	0.84[ASN][1000 genomes]
rs4985969	0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4985970	0.84[ASN][1000 genomes]
rs4985971	0.84[ASN][1000 genomes]
rs56323013	0.90[ASN][1000 genomes]
rs58235085	0.84[ASN][1000 genomes]
rs59543297	0.86[ASN][1000 genomes]
rs59713572	0.87[ASN][1000 genomes]
rs6587111	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587114	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6618	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs719093	0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7209129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7216921	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs899340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9895047	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs9914758	0.86[ASW][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv827917	chr17:20896100-20961777	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9911289	RP11-344E13.3	cis	Heart Left Ventricle	GTEx
rs9911289	FAM27L	cis	parietal	SCAN
rs9911289	MED9	cis	cerebellum	SCAN
rs9911289	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs9911289	GRAP	cis	cerebellum	SCAN
rs9911289	SMCR7	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20900200-20924000	Strong transcription	Fetal Stomach	stomach
2	chr17:20900600-20932400	Strong transcription	Fetal Intestine Small	intestine
3	chr17:20900800-20925600	Strong transcription	Fetal Brain Female	brain
4	chr17:20900800-20932200	Strong transcription	Brain Germinal Matrix	brain
5	chr17:20901400-20912200	Strong transcription	Primary B cells from cord blood	blood
6	chr17:20901400-20925200	Strong transcription	Fetal Lung	lung
7	chr17:20901400-20932600	Strong transcription	Thymus	Thymus
8	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr17:20901800-20929400	Strong transcription	GM12878-XiMat	blood
10	chr17:20901800-20932000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr17:20901800-20932000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr17:20901800-20932400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr17:20901800-20936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:20902000-20925200	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr17:20902000-20932600	Strong transcription	Fetal Intestine Large	intestine
16	chr17:20902000-20935400	Strong transcription	Dnd41	blood
17	chr17:20902200-20918600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr17:20902200-20925200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr17:20902200-20932400	Strong transcription	Fetal Thymus	thymus
20	chr17:20902200-20932600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr17:20902400-20927000	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr17:20902400-20931600	Strong transcription	HMEC	breast
23	chr17:20902400-20932200	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr17:20902400-20932200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr17:20902400-20932600	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr17:20902600-20924200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr17:20902600-20925400	Strong transcription	NHEK	skin
28	chr17:20902600-20932000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr17:20902600-20932200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
30	chr17:20902600-20932400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr17:20902600-20932800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr17:20902800-20909600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr17:20902800-20909600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:20902800-20923600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr17:20902800-20925200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr17:20902800-20925200	Strong transcription	Colonic Mucosa	Colon
37	chr17:20903000-20911000	Genic enhancers	Brain Cingulate Gyrus	brain
38	chr17:20903200-20917000	Strong transcription	Esophagus	oesophagus
39	chr17:20903200-20925200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr17:20903200-20932000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr17:20903400-20932000	Strong transcription	Liver	Liver
42	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr17:20903600-20938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr17:20903800-20924000	Strong transcription	Lung	lung
45	chr17:20903800-20925000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr17:20904000-20910800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr17:20904000-20928200	Strong transcription	A549	lung
48	chr17:20904000-20931600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr17:20904200-20926600	Strong transcription	Primary T cells from cord blood	blood
50	chr17:20904600-20925200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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