Variant report

Variant	rs10255399
Chromosome Location	chr7:98970124-98970125
allele	C/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	POLR2A	chr7:98969974-98970662	HepG2	liver:	n/a	n/a
2	ELF1	chr7:98970007-98970692	MCF-7	breast:	n/a	chr7:98970300-98970313 chr7:98970301-98970312 chr7:98970302-98970311 chr7:98970301-98970312
3	JUN	chr7:98970076-98970508	HepG2	liver:	n/a	n/a
4	POLR2A	chr7:98970113-98970888	K562	blood:	n/a	n/a
5	EP300	chr7:98969850-98970686	ECC-1	luminal epithelium:	n/a	chr7:98970638-98970648
6	CEBPB	chr7:98969888-98970321	K562	blood:	n/a	chr7:98970088-98970099
7	HEY1	chr7:98969988-98970627	HepG2	liver:	n/a	n/a
8	HEY1	chr7:98970103-98970607	HepG2	liver:	n/a	n/a
9	EP300	chr7:98970071-98970656	HepG2	liver:	n/a	chr7:98970638-98970648
10	CEBPB	chr7:98969911-98970590	HepG2	liver:	n/a	chr7:98970088-98970099
11	CEBPB	chr7:98969917-98970581	HepG2	liver:	n/a	chr7:98970088-98970099
12	CEBPB	chr7:98969909-98970275	Hela-S3	cervix:	n/a	chr7:98970088-98970099
13	CEBPB	chr7:98969934-98970395	A549	lung:	n/a	chr7:98970088-98970099
14	CEBPB	chr7:98969929-98970294	K562	blood:	n/a	chr7:98970088-98970099
15	CEBPB	chr7:98969955-98970202	HepG2	liver:	n/a	chr7:98970088-98970099
16	POLR2A	chr7:98970051-98970569	ECC-1	luminal epithelium:	n/a	n/a
17	RXRA	chr7:98970010-98970685	HepG2	liver:	n/a	chr7:98970298-98970307
18	CEBPB	chr7:98969872-98970452	ECC-1	luminal epithelium:	n/a	chr7:98970088-98970099
19	ELF1	chr7:98969942-98970888	HepG2	liver:	n/a	chr7:98970300-98970313 chr7:98970301-98970312 chr7:98970302-98970311 chr7:98970301-98970312
20	TCF12	chr7:98969865-98970859	ECC-1	luminal epithelium:	n/a	chr7:98970638-98970647
21	USF1	chr7:98970109-98970666	ECC-1	luminal epithelium:	n/a	n/a
22	CEBPB	chr7:98969911-98970499	ECC-1	luminal epithelium:	n/a	chr7:98970088-98970099
23	EP300	chr7:98970113-98970467	HepG2	liver:	n/a	n/a
24	NFIC	chr7:98970117-98970660	HepG2	liver:	n/a	n/a
25	TCF12	chr7:98969904-98970644	ECC-1	luminal epithelium:	n/a	n/a
26	CEBPD	chr7:98969967-98970500	HepG2	liver:	n/a	n/a
27	POLR2A	chr7:98970101-98970638	HepG2	liver:	n/a	n/a
28	MAX	chr7:98969936-98970681	ECC-1	luminal epithelium:	n/a	n/a
29	TBP	chr7:98970014-98970621	HepG2	liver:	n/a	n/a
30	CEBPB	chr7:98969939-98970283	A549	lung:	n/a	chr7:98970088-98970099
31	POLR2A	chr7:98970049-98971023	HepG2	liver:	n/a	n/a
32	ARID3A	chr7:98970074-98970679	HepG2	liver:	n/a	chr7:98970146-98970162
33	MAX	chr7:98969829-98970585	ECC-1	luminal epithelium:	n/a	n/a
34	TEAD4	chr7:98969791-98970743	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr7:98970101-98970585	HepG2	liver:	n/a	n/a
36	HDAC2	chr7:98970055-98970656	HepG2	liver:	n/a	n/a
37	MYBL2	chr7:98969989-98970783	HepG2	liver:	n/a	n/a
38	CEBPB	chr7:98969933-98970279	H1-hESC	embryonic stem cell:	n/a	chr7:98970088-98970099
39	ESR1	chr7:98969976-98970606	ECC-1	luminal epithelium:	n/a	n/a
40	CEBPB	chr7:98969910-98970288	IMR90	lung:	n/a	chr7:98970088-98970099
41	NFIC	chr7:98969873-98970597	ECC-1	luminal epithelium:	n/a	n/a
42	EP300	chr7:98970100-98970613	HepG2	liver:	n/a	n/a
43	TEAD4	chr7:98969895-98970680	HepG2	liver:	n/a	n/a
44	MYBL2	chr7:98969971-98970719	HepG2	liver:	n/a	n/a
45	JUN	chr7:98970054-98970150	K562	blood:	n/a	n/a
46	HNF4G	chr7:98970119-98970520	HepG2	liver:	n/a	chr7:98970319-98970334
47	ELF1	chr7:98969873-98970799	HCT-116	colon:	n/a	chr7:98970300-98970313 chr7:98970301-98970312 chr7:98970302-98970311 chr7:98970301-98970312
48	CEBPB	chr7:98969931-98970377	MCF-7	breast:	n/a	chr7:98970088-98970099
49	CEBPB	chr7:98969918-98970496	HepG2	liver:	n/a	chr7:98970088-98970099
50	CEBPB	chr7:98969903-98970500	MCF-7	breast:	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
ENSG00000130429	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000241685	Chromatin interaction
ENSG00000106244	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10155966	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10236149	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10243678	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10249167	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10258757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10267346	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10270459	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10270917	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10272998	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10274407	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10277149	0.80[EUR][1000 genomes]
rs10279308	0.81[EUR][1000 genomes]
rs10953287	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11762273	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11973460	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11978089	0.81[EUR][1000 genomes]
rs17161698	0.91[ASN][1000 genomes]
rs1985453	0.82[ASN][1000 genomes]
rs2003499	0.80[EUR][1000 genomes]
rs2057905	0.86[ASN][1000 genomes]
rs2057906	0.90[ASN][1000 genomes]
rs2072181	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2107922	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2269985	0.84[ASN][1000 genomes]
rs2286162	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2301889	0.81[ASN][1000 genomes]
rs2404322	0.88[ASN][1000 genomes]
rs2404323	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28468623	0.81[ASN][1000 genomes]
rs28495024	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28820905	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3764815	0.83[ASN][1000 genomes]
rs3801288	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58660994	0.81[ASN][1000 genomes]
rs59986060	0.82[ASN][1000 genomes]
rs6943920	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6953476	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6955490	0.86[EUR][1000 genomes]
rs6972337	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6975099	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73395547	0.81[ASN][1000 genomes]
rs73395557	0.81[ASN][1000 genomes]
rs9641253	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10255399	ARPC1B	cis	Thyroid	GTEx

Chromatin state (count:121 , 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	chr7:98955600-98970200	Weak transcription	Fetal Brain Male	brain
6	chr7:98956200-98970400	Weak transcription	Stomach Mucosa	stomach
7	chr7:98959400-98970400	Weak transcription	Psoas Muscle	Psoas
8	chr7:98959400-98971600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:98961200-98971600	Weak transcription	Small Intestine	intestine
10	chr7:98962200-98971600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:98962800-98971400	Weak transcription	Primary B cells from cord blood	blood
12	chr7:98964400-98970200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:98964600-98970600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr7:98964600-98971600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:98964600-98971600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:98964800-98970200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr7:98964800-98971400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:98964800-98971400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr7:98965000-98970200	Weak transcription	Pancreas	Pancrea
20	chr7:98965000-98970200	Weak transcription	NH-A	brain
21	chr7:98965000-98970200	Weak transcription	NHDF-Ad	bronchial
22	chr7:98965000-98970400	Weak transcription	Fetal Lung	lung
23	chr7:98965000-98970800	Weak transcription	Primary T cells from cord blood	blood
24	chr7:98965000-98971400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr7:98965000-98971600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr7:98965000-98971600	Weak transcription	HMEC	breast
27	chr7:98965000-98971800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:98965000-98971800	Weak transcription	Brain Substantia Nigra	brain
29	chr7:98965200-98970200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr7:98965200-98970200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr7:98965200-98970200	Weak transcription	Liver	Liver
32	chr7:98965200-98970200	Weak transcription	Brain Angular Gyrus	brain
33	chr7:98965200-98970200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr7:98965200-98970200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr7:98965200-98970400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr7:98965200-98970400	Weak transcription	Lung	lung
37	chr7:98965200-98970400	Weak transcription	Ovary	ovary
38	chr7:98965200-98970800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr7:98965200-98970800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr7:98965200-98971400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr7:98965200-98971400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr7:98965200-98971400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr7:98965200-98971400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr7:98965200-98971400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr7:98965200-98971600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr7:98965200-98971600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr7:98965200-98971600	Weak transcription	Aorta	Aorta
48	chr7:98965200-98971600	Weak transcription	Esophagus	oesophagus
49	chr7:98965200-98971600	Weak transcription	Gastric	stomach
50	chr7:98965200-98971600	Weak transcription	HUVEC	blood vessel

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