Variant report

Variant	rs192705
Chromosome Location	chr9:86591704-86591705
allele	C/T
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	POLR2A	chr9:86590978-86591744	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr9:86583469-86597690	K562	blood:	n/a	n/a
3	POLR2A	chr9:86589056-86597036	GM12878	blood:	n/a	n/a
4	POLR2A	chr9:86589423-86592000	GM12878	blood:	n/a	n/a
5	POLR2A	chr9:86589301-86591746	HepG2	liver:	n/a	n/a
6	STAT3	chr9:86591411-86591754	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr9:86589117-86591869	H1-hESC	embryonic stem cell:	n/a	n/a
8	STAT3	chr9:86591418-86591712	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr9:86591266-86593022	U87	brain:	n/a	n/a
10	STAT3	chr9:86591418-86591753	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr9:86584019-86593013	HepG2	liver:	n/a	n/a
12	POLR2A	chr9:86591266-86592530	U87	brain:	n/a	n/a
13	POLR2A	chr9:86591552-86592884	A549	lung:	n/a	n/a
14	FOS	chr9:86591439-86591768	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr9:86591328-86591750	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr9:86591352-86591797	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr9:86584178-86592956	GM12891	blood:	n/a	n/a
18	STAT3	chr9:86591408-86591755	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86535076..86537991-chr9:86590146..86593000,2	K562	blood:

Variant related genes	Relation type
RMI1	TF binding region
HNRNPK	TF binding region
ENSG00000165115	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10780638	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10868074	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10868079	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11140323	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11792634	0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[YRI][hapmap]
rs1572031	0.91[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2065516	0.87[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs2780142	0.80[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs295274	0.91[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs295291	0.91[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap]
rs296885	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4297107	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs6559750	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs7024316	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7026436	0.87[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs754144	0.91[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7869387	0.87[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs7875289	0.87[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs9314723	0.91[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
5	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 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	chr9:86572200-86593200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:86581200-86591800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:86581200-86591800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:86581200-86591800	Strong transcription	HSMMtube	muscle
5	chr9:86581200-86592200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:86581200-86592200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:86581200-86592400	Strong transcription	Fetal Thymus	thymus
8	chr9:86581200-86593000	Strong transcription	Placenta	Placenta
9	chr9:86581400-86591800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:86581400-86592000	Strong transcription	NH-A	brain
11	chr9:86581400-86592000	Strong transcription	NHDF-Ad	bronchial
12	chr9:86581400-86592200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr9:86581400-86592200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr9:86581600-86592200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr9:86581600-86592600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr9:86581800-86591800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr9:86581800-86592200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr9:86581800-86592600	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:86582200-86592800	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr9:86582600-86592200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
21	chr9:86583400-86592000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr9:86583600-86592000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:86583800-86592600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr9:86584200-86591800	Strong transcription	Primary B cells from cord blood	blood
25	chr9:86584600-86592000	Strong transcription	Thymus	Thymus
26	chr9:86584600-86592800	Strong transcription	Colonic Mucosa	Colon
27	chr9:86585800-86592600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr9:86586000-86591800	Strong transcription	Psoas Muscle	Psoas
29	chr9:86586000-86592000	Strong transcription	Primary hematopoietic stem cells	blood
30	chr9:86586000-86592800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:86586600-86592600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr9:86586800-86592200	Genic enhancers	A549	lung
33	chr9:86587400-86592000	Genic enhancers	HepG2	liver
34	chr9:86587400-86592600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr9:86587400-86593000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr9:86587600-86592000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr9:86587600-86592200	Genic enhancers	Primary T cells from cord blood	blood
38	chr9:86588400-86593000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
39	chr9:86588600-86592800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr9:86588600-86592800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr9:86588800-86592200	Weak transcription	Stomach Mucosa	stomach
42	chr9:86589000-86592200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr9:86589200-86593200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:86589400-86592600	Genic enhancers	Hela-S3	cervix
45	chr9:86589600-86591800	Genic enhancers	Brain Germinal Matrix	brain
46	chr9:86589600-86591800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
47	chr9:86589600-86592000	Genic enhancers	Colon Smooth Muscle	Colon
48	chr9:86589600-86592600	Genic enhancers	Brain Hippocampus Middle	brain
49	chr9:86589600-86593000	Genic enhancers	Brain Inferior Temporal Lobe	brain
50	chr9:86589800-86591800	Genic enhancers	HUVEC	blood vessel

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