Variant report

Variant	rs11658178
Chromosome Location	chr17:20923489-20923490
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:20923340-20923490	HCM	heart:	n/a	n/a
2	CTCF	chr17:20923350-20924041	SK-N-SH	brain:	n/a	chr17:20923680-20923698
3	POLR2A	chr17:20923430-20923533	K562	blood:	n/a	n/a
4	RAD21	chr17:20923487-20923960	MCF-7	breast:	n/a	chr17:20923744-20923753
5	RUNX3	chr17:20923478-20923845	GM12878	blood:	n/a	n/a
6	CTCF	chr17:20922989-20924101	A549	lung:	n/a	chr17:20923680-20923698
7	RUNX3	chr17:20923474-20923809	GM12878	blood:	n/a	n/a
8	CTCF	chr17:20923440-20923590	A549	lung:	n/a	n/a
9	ZNF384	chr17:20923455-20923612	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:20922041-20925194	K562	blood:	n/a	n/a
11	POLR2A	chr17:20923462-20924884	GM12892	blood:	n/a	n/a
12	POLR2A	chr17:20923249-20923899	H1-neurons	neurons:	n/a	n/a
13	RAD21	chr17:20923465-20923849	SK-N-SH	brain:	n/a	chr17:20923744-20923753
14	POLR2A	chr17:20922111-20925115	A549	lung:	n/a	n/a
15	RAD21	chr17:20923467-20923905	H1-hESC	embryonic stem cell:	n/a	chr17:20923744-20923753
16	POLR2A	chr17:20919543-20925272	PFSK-1	brain:	n/a	n/a
17	CTCF	chr17:20923440-20923953	MCF-7	breast:	n/a	chr17:20923680-20923698

No.	Distal block	Cell Line	Cell type
1	chr17:20923012..20923975-chr17:21002694..21003451,3	K562	blood:
2	chr17:20923120..20926842-chr17:20942462..20946048,5	K562	blood:
3	chr17:20923032..20923694-chr17:21008464..21009292,2	MCF-7	breast:
4	chr17:20923323..20925346-chr17:20944193..20946472,2	MCF-7	breast:
5	chr17:20922289..20926435-chr17:20942892..20947042,7	MCF-7	breast:

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

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1045215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs10512423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204325	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap]
rs11204327	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11204329	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204331	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11541311	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11650623	0.82[CEU][hapmap]
rs11651078	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11651500	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652224	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11653213	0.89[AMR][1000 genomes]
rs11653504	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11654801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11655512	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes]
rs11655985	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11656525	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11656662	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656874	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11657155	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11658389	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11658671	0.83[ASN][1000 genomes]
rs11658722	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs11658742	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs11658791	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11869271	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11870338	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16942330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16962375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16962469	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes]
rs2009757	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3785544	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3891644	0.91[CHB][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62056764	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62056765	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62056768	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62056770	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62056771	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62056832	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62058987	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62058990	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62058991	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62058993	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62059000	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62059001	0.89[ASN][1000 genomes]
rs716959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7217797	0.83[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes]
rs7218520	0.92[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs7224752	0.84[ASN][1000 genomes]
rs8079468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9905095	1.00[CHB][hapmap]
rs9914432	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs9972887	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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

No data

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	chr17:20901400-20925200	Strong transcription	Fetal Lung	lung
6	chr17:20901400-20932600	Strong transcription	Thymus	Thymus
7	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:20901800-20929400	Strong transcription	GM12878-XiMat	blood
9	chr17:20901800-20932000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr17:20901800-20932000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr17:20901800-20932400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr17:20901800-20936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr17:20902000-20925200	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr17:20902000-20932600	Strong transcription	Fetal Intestine Large	intestine
15	chr17:20902000-20935400	Strong transcription	Dnd41	blood
16	chr17:20902200-20925200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:20902200-20932400	Strong transcription	Fetal Thymus	thymus
18	chr17:20902200-20932600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr17:20902400-20927000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr17:20902400-20931600	Strong transcription	HMEC	breast
21	chr17:20902400-20932200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr17:20902400-20932200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr17:20902400-20932600	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr17:20902600-20924200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr17:20902600-20925400	Strong transcription	NHEK	skin
26	chr17:20902600-20932000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr17:20902600-20932200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr17:20902600-20932400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr17:20902600-20932800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr17:20902800-20923600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr17:20902800-20925200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr17:20902800-20925200	Strong transcription	Colonic Mucosa	Colon
33	chr17:20903200-20925200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr17:20903200-20932000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr17:20903400-20932000	Strong transcription	Liver	Liver
36	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:20903600-20938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:20903800-20924000	Strong transcription	Lung	lung
39	chr17:20903800-20925000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
40	chr17:20904000-20928200	Strong transcription	A549	lung
41	chr17:20904000-20931600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr17:20904200-20926600	Strong transcription	Primary T cells from cord blood	blood
43	chr17:20904600-20925200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr17:20904600-20925200	Strong transcription	NH-A	brain
45	chr17:20904800-20924800	Strong transcription	Fetal Kidney	kidney
46	chr17:20905000-20923800	Strong transcription	Pancreas	Pancrea
47	chr17:20905000-20925200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr17:20905000-20933000	Strong transcription	Hela-S3	cervix
49	chr17:20905200-20926600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr17:20905400-20925200	Strong transcription	Muscle Satellite Cultured Cells	--

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