Variant report

Variant	rs17086750
Chromosome Location	chr9:86593815-86593816
allele	G/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	chr9:86593110-86595750	A549	lung:	n/a	n/a
2	MXI1	chr9:86593619-86596557	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr9:86593061-86596929	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr9:86593527-86596747	GM12878	blood:	n/a	n/a
5	POLR2A	chr9:86592005-86597005	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr9:86583469-86597690	K562	blood:	n/a	n/a
7	POLR2A	chr9:86589056-86597036	GM12878	blood:	n/a	n/a
8	POLR2A	chr9:86593589-86596833	GM12892	blood:	n/a	n/a
9	POLR2A	chr9:86593242-86595931	U87	brain:	n/a	n/a
10	NFATC1	chr9:86592763-86594905	GM12878	blood:	n/a	n/a
11	POLR2A	chr9:86593710-86596695	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr9:86593185-86597118	GM12878	blood:	n/a	n/a
13	PML	chr9:86593804-86596661	GM12878	blood:	n/a	n/a
14	SIN3A	chr9:86592976-86596804	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr9:86593770-86596761	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr9:86593791-86596772	Hela-S3	cervix:	n/a	n/a
17	NFATC1	chr9:86592990-86596378	GM12878	blood:	n/a	n/a
18	POLR2A	chr9:86593618-86596491	HUVEC	blood vessel:	n/a	n/a
19	MTA3	chr9:86593815-86597026	GM12878	blood:	n/a	n/a
20	POLR2A	chr9:86593233-86595960	HCT-116	colon:	n/a	n/a
21	SIN3AK20	chr9:86593753-86596939	MCF-7	breast:	n/a	n/a
22	POLR2A	chr9:86593285-86595900	HepG2	liver:	n/a	n/a
23	GATA1	chr9:86593729-86596054	PBDE	blood:	n/a	chr9:86594309-86594318 chr9:86594306-86594316 chr9:86594791-86594801 chr9:86594309-86594318 chr9:86594535-86594545 chr9:86594308-86594318
24	MAZ	chr9:86593616-86596309	IMR90	lung:	n/a	chr9:86594612-86594619 chr9:86595614-86595624 chr9:86595618-86595628
25	POLR2A	chr9:86593736-86595997	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr9:86593306-86596828	HepG2	liver:	n/a	n/a
27	POLR2A	chr9:86593200-86596145	U87	brain:	n/a	n/a
28	POLR2A	chr9:86593507-86596751	IMR90	lung:	n/a	n/a
29	POLR2A	chr9:86593339-86596844	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr9:86593815-86596732	MCF-7	breast:	n/a	n/a
31	POLR2A	chr9:86593702-86596806	PANC-1	pancreas:	n/a	n/a
32	CHD1	chr9:86593158-86596789	IMR90	lung:	n/a	chr9:86595578-86595587 chr9:86596056-86596066 chr9:86595550-86595560 chr9:86595273-86595283
33	POLR2A	chr9:86593648-86595989	HepG2	liver:	n/a	n/a
34	POLR2A	chr9:86593722-86596959	GM12892	blood:	n/a	n/a
35	MXI1	chr9:86593530-86597131	IMR90	lung:	n/a	n/a
36	TBL1XR1	chr9:86593395-86595834	K562	blood:	n/a	n/a
37	POLR2A	chr9:86593190-86596233	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr9:86593715-86596673	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr9:86593206-86596139	U87	brain:	n/a	n/a
40	MXI1	chr9:86593527-86596606	GM12878	blood:	n/a	n/a
41	POLR2A	chr9:86593808-86596918	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr9:86593596-86596794	K562	blood:	n/a	n/a
43	REST	chr9:86593207-86597147	H1-neurons	neurons:	n/a	chr9:86595761-86595774 chr9:86596021-86596039 chr9:86594642-86594655
44	POLR2A	chr9:86593163-86597264	GM12891	blood:	n/a	n/a
45	CHD1	chr9:86592725-86596929	H1-hESC	embryonic stem cell:	n/a	chr9:86595578-86595587 chr9:86596056-86596066 chr9:86595550-86595560 chr9:86595273-86595283
46	POLR2A	chr9:86593602-86596762	K562	blood:	n/a	n/a
47	TBL1XR1	chr9:86593558-86596029	GM12878	blood:	n/a	n/a
48	POLR2A	chr9:86593651-86595962	HUVEC	blood vessel:	n/a	n/a
49	HCFC1	chr9:86593604-86596707	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr9:86593040-86596859	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:62432743..62434322-chr9:86593092..86595353,2	MCF-7	breast:
2	chr9:86320289..86324589-chr9:86593742..86599530,6	K562	blood:
3	chr9:86533593..86537892-chr9:86593047..86598677,10	K562	blood:
4	chr9:86593378..86594996-chr9:86858039..86859653,2	MCF-7	breast:
5	chr9:86319810..86324349-chr9:86592631..86598226,6	K562	blood:
6	chr17:57914983..57917065-chr9:86592190..86594994,2	MCF-7	breast:
7	chr9:86534520..86537940-chr9:86592614..86595774,6	K562	blood:
8	chr9:86593375..86596264-chr9:101558546..101560057,2	MCF-7	breast:
9	chr9:86592736..86597542-chr9:86606160..86610925,6	K562	blood:
10	chr9:86533247..86537973-chr9:86593370..86597981,20	MCF-7	breast:

Variant related genes	Relation type
HNRNPK	TF binding region
RMI1	TF binding region
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000165115	Chromatin interaction
ENSG00000202523	Chromatin interaction
ENSG00000165138	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10868072	0.82[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap]
rs11140298	0.87[GIH][hapmap];0.92[TSI][hapmap]
rs12001293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12001505	0.86[EUR][1000 genomes]
rs12001918	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs12003101	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs12003500	0.86[EUR][1000 genomes]
rs12004444	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12552069	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs17064724	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs2184086	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs34690696	0.88[EUR][1000 genomes]
rs35784768	0.88[EUR][1000 genomes]
rs4480186	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs55872219	0.89[EUR][1000 genomes]
rs56055736	0.87[EUR][1000 genomes]
rs57267691	0.86[EUR][1000 genomes]
rs57957686	0.84[EUR][1000 genomes]
rs58248061	0.84[EUR][1000 genomes]
rs58474042	0.91[EUR][1000 genomes]
rs60277614	0.86[EUR][1000 genomes]
rs61490202	0.84[EUR][1000 genomes]
rs7021609	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs7027121	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs7038235	0.88[EUR][1000 genomes]
rs7040843	0.84[EUR][1000 genomes]
rs7045525	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7046229	0.90[EUR][1000 genomes]
rs7047702	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7048626	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs72749137	0.85[ASN][1000 genomes]
rs73463327	0.84[EUR][1000 genomes]
rs73463379	0.88[EUR][1000 genomes]
rs73463395	0.91[EUR][1000 genomes]
rs73469343	0.93[EUR][1000 genomes]
rs7849708	0.81[EUR][1000 genomes]
rs7850288	0.84[EUR][1000 genomes]
rs7850404	0.84[EUR][1000 genomes]
rs7850640	0.90[EUR][1000 genomes]
rs7853625	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7854432	0.90[EUR][1000 genomes]
rs7856614	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7857619	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs7859830	0.88[EUR][1000 genomes]
rs7859928	0.81[EUR][1000 genomes]
rs7867221	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7874481	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs970846	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17086750	RMI1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86590000-86594400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr9:86590600-86594000	Weak transcription	Spleen	Spleen
3	chr9:86590800-86594400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:86591000-86594400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
5	chr9:86591200-86594400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
6	chr9:86591400-86594400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:86591400-86594600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
8	chr9:86591600-86596600	Active TSS	Ovary	ovary
9	chr9:86591800-86597000	Active TSS	Psoas Muscle	Psoas
10	chr9:86592000-86594200	Transcr. at gene 5' and 3'	K562	blood
11	chr9:86592200-86594400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:86592200-86594400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
13	chr9:86592200-86594400	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
14	chr9:86592200-86594400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
15	chr9:86592200-86594400	Transcr. at gene 5' and 3'	A549	lung
16	chr9:86592200-86594600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:86592200-86596800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:86592200-86597000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:86592400-86594200	Transcr. at gene 5' and 3'	Osteobl	bone
20	chr9:86592400-86596200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
21	chr9:86592400-86596400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr9:86592400-86596600	Active TSS	Aorta	Aorta
23	chr9:86592400-86596800	Active TSS	Right Ventricle	heart
24	chr9:86592400-86597600	Active TSS	Fetal Brain Female	brain
25	chr9:86592600-86596200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:86592600-86596400	Active TSS	HSMMtube	muscle
27	chr9:86592600-86596600	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr9:86592600-86596600	Active TSS	Thymus	Thymus
29	chr9:86592600-86596800	Active TSS	Right Atrium	heart
30	chr9:86592600-86597000	Active TSS	Stomach Smooth Muscle	stomach
31	chr9:86592800-86594000	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr9:86592800-86594000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:86592800-86595000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
34	chr9:86592800-86595400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:86592800-86596400	Active TSS	Fetal Muscle Leg	muscle
36	chr9:86592800-86596400	Active TSS	Placenta Amnion	Placenta Amnion
37	chr9:86592800-86596400	Active TSS	HMEC	breast
38	chr9:86592800-86596600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr9:86592800-86596600	Active TSS	Fetal Intestine Large	intestine
40	chr9:86592800-86596600	Active TSS	Fetal Intestine Small	intestine
41	chr9:86592800-86596800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr9:86592800-86597200	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr9:86592800-86597200	Active TSS	NHLF	lung
44	chr9:86593000-86594000	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr9:86593000-86594000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:86593000-86594200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:86593000-86594400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr9:86593000-86594400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr9:86593000-86596200	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr9:86593000-86596400	Active TSS	Primary T helper naive cells from peripheral blood	blood

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