Variant report

Variant	rs10155966
Chromosome Location	chr7:98981233-98981234
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:98981010-98982518	GM12892	blood:	n/a	n/a
2	PML	chr7:98980873-98982039	GM12878	blood:	n/a	n/a
3	STAT5A	chr7:98980756-98982600	GM12878	blood:	n/a	n/a
4	MTA3	chr7:98980880-98982543	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:98980901-98982549	K562	blood:	n/a	n/a
6	POLR2A	chr7:98981073-98982528	K562	blood:	n/a	n/a
7	POLR2A	chr7:98980835-98982546	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr7:98981225-98981545	GM12891	blood:	n/a	n/a
9	POLR2A	chr7:98981229-98982199	HepG2	liver:	n/a	n/a
10	POLR2A	chr7:98980794-98982466	GM19193	blood:	n/a	n/a
11	POLR2A	chr7:98980807-98982541	GM12891	blood:	n/a	n/a
12	POLR2A	chr7:98981183-98981269	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr7:98980920-98982053	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:98980756-98982534	GM12892	blood:	n/a	n/a
15	POLR2A	chr7:98981165-98982454	GM12878	blood:	n/a	n/a
16	POLR2A	chr7:98981123-98981262	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr7:98981201-98981431	A549	lung:	n/a	n/a
18	NFATC1	chr7:98980926-98982407	GM12878	blood:	n/a	n/a
19	POLR2A	chr7:98980912-98982534	GM12878	blood:	n/a	n/a
20	NFATC1	chr7:98980895-98981750	GM12878	blood:	n/a	n/a
21	POLR2A	chr7:98980876-98982482	GM18505	blood:	n/a	n/a
22	POLR2A	chr7:98981220-98981498	A549	lung:	n/a	n/a
23	POLR2A	chr7:98980830-98982448	K562	blood:	n/a	n/a
24	POLR2A	chr7:98980942-98982082	K562	blood:	n/a	n/a
25	POLR2A	chr7:98980909-98982544	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr7:98981096-98982535	GM12891	blood:	n/a	n/a
27	POLR2A	chr7:98981140-98981869	U87	brain:	n/a	n/a
28	POLR2A	chr7:98981114-98982064	GM12891	blood:	n/a	n/a
29	POLR2A	chr7:98980924-98982337	K562	blood:	n/a	n/a
30	POLR2A	chr7:98981150-98982491	K562	blood:	n/a	n/a
31	POLR2A	chr7:98980800-98982513	GM12892	blood:	n/a	n/a
32	POLR2A	chr7:98980951-98982460	K562	blood:	n/a	n/a
33	POLR2A	chr7:98980793-98981514	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr7:98980833-98982465	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr7:98980703-98982534	GM12878	blood:	n/a	n/a
36	POLR2A	chr7:98980970-98982485	A549	lung:	n/a	n/a
37	POLR2A	chr7:98981098-98982469	GM18951	blood:	n/a	n/a
38	POLR2A	chr7:98981055-98982492	HL-60	blood:	n/a	n/a
39	POLR2A	chr7:98981142-98982431	GM12878	blood:	n/a	n/a
40	POLR2A	chr7:98980936-98982447	GM12892	blood:	n/a	n/a
41	ZKSCAN1	chr7:98980866-98981275	Hela-S3	cervix:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:98980782..98982462-chr7:99001543..99003886,2	MCF-7	breast:
2	chr7:98978155..98981581-chr7:99004279..99007902,6	MCF-7	breast:
3	chr7:98981217..98982817-chr7:98983195..98985825,2	MCF-7	breast:
4	chr7:98978195..98983060-chr7:98988487..98993755,6	MCF-7	breast:

No data

Variant related genes	Relation type
ARPC1B	TF binding region
ENSG00000106244	Chromatin interaction
ENSG00000130429	Chromatin interaction
ENSG00000106245	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10236149	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10238965	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs10243678	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10244158	0.80[AMR][1000 genomes]
rs10249167	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10255399	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10258757	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10267346	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10270459	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10270917	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10271049	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs10272998	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10274407	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10277149	0.81[EUR][1000 genomes]
rs10279308	0.91[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs1043466	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs10953286	0.88[GIH][hapmap];1.00[YRI][hapmap]
rs10953287	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11762273	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11771702	0.83[CEU][hapmap]
rs11772470	0.83[JPT][hapmap]
rs11973460	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11976018	0.91[ASW][hapmap];0.92[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap]
rs11978089	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs12112936	0.83[CEU][hapmap]
rs12113440	0.83[CEU][hapmap]
rs13227795	0.80[AMR][1000 genomes]
rs13240600	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs17161695	0.83[CEU][hapmap]
rs17161698	0.82[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs1980307	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs1985453	0.82[CHD][hapmap]
rs2003499	0.91[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2057905	0.83[ASN][1000 genomes]
rs2057906	0.86[ASN][1000 genomes]
rs2072181	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2107922	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2240384	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs2269985	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2272168	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs2280600	0.83[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs2280601	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs2286162	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2404322	0.85[ASN][1000 genomes]
rs2404323	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404324	0.89[AFR][1000 genomes]
rs28457808	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs28495024	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28820905	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3137	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs3764815	0.90[CHD][hapmap];0.89[JPT][hapmap]
rs3779354	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs3801288	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3843540	0.83[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap]
rs4729532	0.92[ASW][hapmap];0.91[CEU][hapmap];0.81[MKK][hapmap];0.80[EUR][1000 genomes]
rs6943920	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6953476	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6955490	0.92[ASW][hapmap];0.91[CEU][hapmap];0.81[MKK][hapmap];0.84[EUR][1000 genomes]
rs6962772	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs6972337	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6975099	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs733991	0.83[CEU][hapmap]
rs7794682	0.80[AMR][1000 genomes]
rs7794705	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs883403	0.92[CEU][hapmap];0.80[AMR][1000 genomes]
rs917154	0.91[ASW][hapmap];0.91[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9641253	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9768020	0.87[AMR][1000 genomes];0.80[EUR][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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10155966	ZKSCAN1	cis	parietal	SCAN
rs10155966	ACTL6B	cis	cerebellum	SCAN
rs10155966	PILRA	cis	cerebellum	SCAN
rs10155966	OR2AE1	cis	parietal	SCAN
rs10155966	CPSF4	cis	parietal	SCAN
rs10155966	GATS	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98971000-98990400	Weak transcription	Fetal Kidney	kidney
2	chr7:98973400-98984000	Weak transcription	Aorta	Aorta
3	chr7:98973400-98984200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:98973400-98984200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:98973400-98984200	Weak transcription	Ovary	ovary
6	chr7:98973400-98984400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr7:98973400-98987400	Weak transcription	Brain Germinal Matrix	brain
8	chr7:98973400-98987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:98973400-98989800	Weak transcription	Brain Angular Gyrus	brain
10	chr7:98977800-98984000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:98977800-98984200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr7:98978000-98984200	Weak transcription	HSMMtube	muscle
13	chr7:98978000-98987000	Weak transcription	Small Intestine	intestine
14	chr7:98978200-98984000	Weak transcription	Fetal Lung	lung
15	chr7:98978200-98984200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr7:98978200-98989800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:98978400-98983200	Weak transcription	Fetal Intestine Large	intestine
18	chr7:98978400-98984000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:98978400-98984200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:98978400-98984200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:98978600-98983600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr7:98978600-98984400	Weak transcription	NH-A	brain
23	chr7:98978800-98985000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:98978800-98989000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:98979000-98982000	Strong transcription	Osteobl	bone
26	chr7:98979000-98983200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:98979000-98983200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:98979000-98984000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:98979000-98984000	Weak transcription	Brain Hippocampus Middle	brain
30	chr7:98979000-98984600	Genic enhancers	Primary monocytes fromperipheralblood	blood
31	chr7:98979000-98989600	Weak transcription	Stomach Mucosa	stomach
32	chr7:98979200-98981600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:98979200-98983000	Weak transcription	HMEC	breast
34	chr7:98979200-98983400	Genic enhancers	Primary B cells from cord blood	blood
35	chr7:98979200-98983400	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr7:98979200-98983800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr7:98979200-98984000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:98979200-98984000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr7:98979200-98984000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:98979200-98984200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr7:98979200-98984200	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr7:98979200-98984400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr7:98979200-98987000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr7:98979200-98987000	Weak transcription	HSMM	muscle
45	chr7:98979200-98989600	Weak transcription	Brain Substantia Nigra	brain
46	chr7:98979400-98983000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr7:98979400-98983000	Weak transcription	HUVEC	blood vessel
48	chr7:98979400-98983200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr7:98979400-98983200	Weak transcription	Hela-S3	cervix
50	chr7:98979400-98983400	Enhancers	Primary T helper cells PMA-I stimulated	--

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