Variant report

Variant	rs10270917
Chromosome Location	chr7:98970214-98970215
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	chr7:98969974-98970662	HepG2	liver:	n/a	n/a
2	SIN3AK20	chr7:98970140-98970541	HepG2	liver:	n/a	n/a
3	ELF1	chr7:98970007-98970692	MCF-7	breast:	n/a	chr7:98970300-98970313 chr7:98970301-98970312 chr7:98970302-98970311 chr7:98970301-98970312
4	MAZ	chr7:98970176-98970616	HepG2	liver:	n/a	n/a
5	JUN	chr7:98970076-98970508	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:98970113-98970888	K562	blood:	n/a	n/a
7	EP300	chr7:98969850-98970686	ECC-1	luminal epithelium:	n/a	chr7:98970638-98970648
8	CEBPB	chr7:98969888-98970321	K562	blood:	n/a	chr7:98970088-98970099
9	SMC3	chr7:98970139-98970531	HepG2	liver:	n/a	n/a
10	HEY1	chr7:98969988-98970627	HepG2	liver:	n/a	n/a
11	HEY1	chr7:98970103-98970607	HepG2	liver:	n/a	n/a
12	EP300	chr7:98970071-98970656	HepG2	liver:	n/a	chr7:98970638-98970648
13	POLR2A	chr7:98970158-98970681	HepG2	liver:	n/a	n/a
14	MAFK	chr7:98970207-98970453	HepG2	liver:	n/a	n/a
15	CEBPB	chr7:98969911-98970590	HepG2	liver:	n/a	chr7:98970088-98970099
16	CEBPB	chr7:98969917-98970581	HepG2	liver:	n/a	chr7:98970088-98970099
17	CEBPB	chr7:98969909-98970275	Hela-S3	cervix:	n/a	chr7:98970088-98970099
18	CEBPB	chr7:98969934-98970395	A549	lung:	n/a	chr7:98970088-98970099
19	CEBPB	chr7:98969929-98970294	K562	blood:	n/a	chr7:98970088-98970099
20	USF1	chr7:98970143-98970601	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr7:98970051-98970569	ECC-1	luminal epithelium:	n/a	n/a
22	RXRA	chr7:98970010-98970685	HepG2	liver:	n/a	chr7:98970298-98970307
23	CEBPB	chr7:98969872-98970452	ECC-1	luminal epithelium:	n/a	chr7:98970088-98970099
24	ELF1	chr7:98969942-98970888	HepG2	liver:	n/a	chr7:98970300-98970313 chr7:98970301-98970312 chr7:98970302-98970311 chr7:98970301-98970312
25	TCF12	chr7:98969865-98970859	ECC-1	luminal epithelium:	n/a	chr7:98970638-98970647
26	USF1	chr7:98970109-98970666	ECC-1	luminal epithelium:	n/a	n/a
27	CEBPB	chr7:98969911-98970499	ECC-1	luminal epithelium:	n/a	chr7:98970088-98970099
28	EP300	chr7:98970113-98970467	HepG2	liver:	n/a	n/a
29	NFIC	chr7:98970117-98970660	HepG2	liver:	n/a	n/a
30	TCF12	chr7:98969904-98970644	ECC-1	luminal epithelium:	n/a	n/a
31	CEBPD	chr7:98969967-98970500	HepG2	liver:	n/a	n/a
32	POLR2A	chr7:98970101-98970638	HepG2	liver:	n/a	n/a
33	MAX	chr7:98969936-98970681	ECC-1	luminal epithelium:	n/a	n/a
34	TBP	chr7:98970014-98970621	HepG2	liver:	n/a	n/a
35	CEBPB	chr7:98969939-98970283	A549	lung:	n/a	chr7:98970088-98970099
36	POLR2A	chr7:98970049-98971023	HepG2	liver:	n/a	n/a
37	POLR2A	chr7:98970126-98970476	HCT-116	colon:	n/a	n/a
38	RXRA	chr7:98970182-98970666	HepG2	liver:	n/a	chr7:98970298-98970307
39	ARID3A	chr7:98970074-98970679	HepG2	liver:	n/a	chr7:98970146-98970162
40	MAX	chr7:98969829-98970585	ECC-1	luminal epithelium:	n/a	n/a
41	MXI1	chr7:98970127-98970705	HepG2	liver:	n/a	n/a
42	TEAD4	chr7:98969791-98970743	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr7:98970101-98970585	HepG2	liver:	n/a	n/a
44	FOXA2	chr7:98970165-98970507	HepG2	liver:	n/a	n/a
45	POLR2A	chr7:98970149-98970990	PANC-1	pancreas:	n/a	n/a
46	HDAC2	chr7:98970055-98970656	HepG2	liver:	n/a	n/a
47	MYBL2	chr7:98969989-98970783	HepG2	liver:	n/a	n/a
48	TEAD4	chr7:98970133-98970429	HepG2	liver:	n/a	n/a
49	POLR2A	chr7:98970200-98970330	HepG2	liver:	n/a	n/a
50	CEBPB	chr7:98969933-98970279	H1-hESC	embryonic stem cell:	n/a	chr7:98970088-98970099

No.	Distal block	Cell Line	Cell type
1	chr7:98921655..98927239-chr7:98969297..98973851,7	MCF-7	breast:
2	chr7:98964264..98966254-chr7:98968520..98970392,2	K562	blood:
3	chr7:98968876..98974378-chr7:99004810..99008269,11	K562	blood:
4	chr7:98966757..98974253-chr7:98988800..98995304,7	K562	blood:
5	chr7:98959822..98968172-chr7:98968902..98974586,14	MCF-7	breast:

Variant related genes	Relation type
ARPC1B	TF binding region
ENSG00000106244	Chromatin interaction
ENSG00000130429	Chromatin interaction
ENSG00000241685	Chromatin interaction
ENSG00000106245	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10155966	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]
rs10236149	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10238965	0.92[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap]
rs10243678	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[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];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10249167	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10255399	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10258757	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10267346	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10270459	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10271049	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap]
rs10272998	0.91[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10274407	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10277149	0.80[EUR][1000 genomes]
rs10279308	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1043466	0.92[CEU][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap]
rs10953286	0.91[GIH][hapmap];1.00[YRI][hapmap]
rs10953287	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11762273	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11771702	0.83[CEU][hapmap]
rs11973460	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11976018	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap]
rs11978089	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs12112936	0.83[CEU][hapmap]
rs12113440	0.83[CEU][hapmap]
rs13240600	0.82[CEU][hapmap];0.89[JPT][hapmap]
rs17161695	0.83[CEU][hapmap]
rs17161698	0.91[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1980307	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap]
rs1985453	0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs2003499	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs2057905	0.84[ASN][1000 genomes]
rs2057906	0.88[ASN][1000 genomes]
rs2072181	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2107922	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2240384	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap]
rs2269985	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2272168	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs2280600	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap]
rs2280601	0.92[CEU][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap]
rs2286162	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2301889	0.82[CHD][hapmap]
rs2404322	0.87[ASN][1000 genomes]
rs2404323	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28495024	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28820905	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3137	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs3764815	0.90[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs3779354	0.89[JPT][hapmap]
rs3801288	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3843540	0.83[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs4729532	0.91[CEU][hapmap]
rs59986060	0.80[ASN][1000 genomes]
rs6943920	0.82[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6953476	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6955490	0.91[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs6962772	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap]
rs6972337	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6975099	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs733991	0.83[CEU][hapmap]
rs7794705	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs883403	0.92[CEU][hapmap]
rs917154	0.91[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap]
rs9641253	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9768020	0.88[AMR][1000 genomes];0.81[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10270917	ACTL6B	cis	cerebellum	SCAN
rs10270917	OR2AE1	cis	parietal	SCAN
rs10270917	CPSF4	cis	parietal	SCAN
rs10270917	PILRA	cis	cerebellum	SCAN
rs10270917	ARPC1B	cis	Thyroid	GTEx
rs10270917	ZKSCAN1	cis	parietal	SCAN
rs10270917	GATS	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98924600-98971600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:98935600-98971600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:98953800-98971600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:98955000-98971600	Weak transcription	Right Atrium	heart
5	chr7:98956200-98970400	Weak transcription	Stomach Mucosa	stomach
6	chr7:98959400-98970400	Weak transcription	Psoas Muscle	Psoas
7	chr7:98959400-98971600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:98961200-98971600	Weak transcription	Small Intestine	intestine
9	chr7:98962200-98971600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:98962800-98971400	Weak transcription	Primary B cells from cord blood	blood
11	chr7:98964600-98970600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr7:98964600-98971600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:98964600-98971600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:98964800-98971400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:98964800-98971400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr7:98965000-98970400	Weak transcription	Fetal Lung	lung
17	chr7:98965000-98970800	Weak transcription	Primary T cells from cord blood	blood
18	chr7:98965000-98971400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr7:98965000-98971600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr7:98965000-98971600	Weak transcription	HMEC	breast
21	chr7:98965000-98971800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr7:98965000-98971800	Weak transcription	Brain Substantia Nigra	brain
23	chr7:98965200-98970400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr7:98965200-98970400	Weak transcription	Lung	lung
25	chr7:98965200-98970400	Weak transcription	Ovary	ovary
26	chr7:98965200-98970800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr7:98965200-98970800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr7:98965200-98971400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr7:98965200-98971400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr7:98965200-98971400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr7:98965200-98971400	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr7:98965200-98971400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr7:98965200-98971600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr7:98965200-98971600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:98965200-98971600	Weak transcription	Aorta	Aorta
36	chr7:98965200-98971600	Weak transcription	Esophagus	oesophagus
37	chr7:98965200-98971600	Weak transcription	Gastric	stomach
38	chr7:98965200-98971600	Weak transcription	HUVEC	blood vessel
39	chr7:98965200-98971800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr7:98965400-98971600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr7:98966600-98971200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr7:98966600-98971600	Weak transcription	GM12878-XiMat	blood
43	chr7:98966800-98971600	Weak transcription	Dnd41	blood
44	chr7:98966800-98971800	Weak transcription	Hela-S3	cervix
45	chr7:98967000-98971400	Weak transcription	A549	lung
46	chr7:98967200-98971000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr7:98967200-98971600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr7:98967400-98970400	Weak transcription	Right Ventricle	heart
49	chr7:98967400-98971800	Weak transcription	Brain Germinal Matrix	brain
50	chr7:98967600-98971600	Weak transcription	Stomach Smooth Muscle	stomach

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