Variant report

Variant	rs12087862
Chromosome Location	chr1:113162436-113162437
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:480)
CpG islands
(count:0)
Chromatin interactive
region (count:48)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:480 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr1:113162135-113162489	A549	lung:	n/a	n/a
2	GTF2F1	chr1:113161201-113163088	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:113160837-113163847	U87	brain:	n/a	n/a
4	SP4	chr1:113162103-113162732	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr1:113161303-113162976	A549	lung:	n/a	chr1:113161493-113161507 chr1:113161499-113161510 chr1:113161725-113161745
6	TAF1	chr1:113162120-113162953	GM12891	blood:	n/a	n/a
7	POLR2A	chr1:113161333-113162804	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr1:113162164-113162876	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:113161133-113163330	HepG2	liver:	n/a	n/a
10	PBX3	chr1:113162044-113162654	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr1:113160770-113163442	U87	brain:	n/a	n/a
12	POLR2A	chr1:113161189-113163081	ProgFib	skin:	n/a	n/a
13	NR2F2	chr1:113161118-113163240	K562	blood:	n/a	n/a
14	TEAD4	chr1:113160214-113163630	K562	blood:	n/a	n/a
15	GATA2	chr1:113161568-113162607	SH-SY5Y	brain:	n/a	n/a
16	FOS	chr1:113162114-113162503	MCF10A-Er-Src	breast:	n/a	n/a
17	MAX	chr1:113161375-113162963	HepG2	liver:	n/a	chr1:113161496-113161506
18	NFYA	chr1:113162242-113162524	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:113160211-113163888	IMR90	lung:	n/a	n/a
20	MAX	chr1:113160603-113163265	Hela-S3	cervix:	n/a	chr1:113161496-113161506
21	POLR2A	chr1:113161319-113163804	K562	blood:	n/a	n/a
22	ZNF143	chr1:113161621-113163060	Hela-S3	cervix:	n/a	n/a
23	TAF7	chr1:113162377-113162777	K562	blood:	n/a	n/a
24	GABPA	chr1:113162186-113162522	HepG2	liver:	n/a	n/a
25	TBP	chr1:113161266-113163037	HepG2	liver:	n/a	n/a
26	GABPA	chr1:113162221-113162466	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:113160541-113163765	GM18505	blood:	n/a	n/a
28	POLR2A	chr1:113160565-113163551	K562	blood:	n/a	n/a
29	RFX5	chr1:113161418-113163150	Hela-S3	cervix:	n/a	n/a
30	BRCA1	chr1:113162100-113162504	H1-hESC	embryonic stem cell:	n/a	n/a
31	CEBPB	chr1:113162212-113163016	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:113160776-113163847	U87	brain:	n/a	n/a
33	JUN	chr1:113162155-113163248	K562	blood:	n/a	n/a
34	MAX	chr1:113161376-113163163	GM12878	blood:	n/a	chr1:113161496-113161506
35	ETS1	chr1:113161940-113162700	GM12878	blood:	n/a	n/a
36	CREB1	chr1:113161943-113162611	ECC-1	luminal epithelium:	n/a	n/a
37	MTA3	chr1:113160468-113163707	GM12878	blood:	n/a	n/a
38	STAT5A	chr1:113161047-113163229	GM12878	blood:	n/a	chr1:113161497-113161509
39	CREB1	chr1:113161464-113162713	HepG2	liver:	n/a	n/a
40	EP300	chr1:113162196-113162546	SK-N-SH_RA	brain:	n/a	n/a
41	TAF1	chr1:113162110-113162887	GM12878	blood:	n/a	n/a
42	ELF1	chr1:113162072-113162594	HepG2	liver:	n/a	n/a
43	POLR2A	chr1:113160712-113163186	GM12878	blood:	n/a	n/a
44	YY1	chr1:113161255-113163101	K562	blood:	n/a	chr1:113161493-113161507 chr1:113161499-113161510 chr1:113161725-113161745
45	YY1	chr1:113161330-113162971	NT2-D1	testis:	n/a	chr1:113161493-113161507 chr1:113161499-113161510 chr1:113161725-113161745
46	CHD1	chr1:113160361-113165418	GM12878	blood:	n/a	n/a
47	HEY1	chr1:113162148-113162662	HepG2	liver:	n/a	n/a
48	SIN3AK20	chr1:113162107-113162534	HepG2	liver:	n/a	n/a
49	TAF1	chr1:113162208-113162738	HepG2	liver:	n/a	n/a
50	POLR2A	chr1:113160679-113163211	GM18951	blood:	n/a	n/a

No data

(count:48 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:112934882..112939118-chr1:113160574..113165273,5	K562	blood:
2	chr1:113162176..113162987-chr3:5163752..5164612,2	Hela-S3	cervix:
3	chr1:113161978..113164385-chr9:33816477..33818971,2	MCF-7	breast:
4	chr1:113006478..113010487-chr1:113159582..113162671,3	K562	blood:
5	chr1:112930309..112940640-chr1:113155859..113164847,24	MCF-7	breast:
6	chr1:113160176..113163931-chr1:113238020..113242018,6	K562	blood:
7	chr1:113162232..113162910-chr7:100463855..100464773,2	Hela-S3	cervix:
8	chr1:113161754..113162459-chr12:122985188..122985790,2	Hela-S3	cervix:
9	chr1:113160443..113165363-chr1:113242054..113245654,5	K562	blood:
10	chr1:113161396..113162589-chr21:34914518..34915250,3	Hela-S3	cervix:
11	chr1:113160312..113164959-chr1:113166253..113170624,10	MCF-7	breast:
12	chr1:113162034..113162837-chr11:66079835..66080745,2	HCT-116	colon:
13	chr1:113002255..113010411-chr1:113160144..113164475,13	MCF-7	breast:
14	chr1:113161304..113162931-chr1:113498706..113500285,2	K562	blood:
15	chr1:113161875..113162734-chr5:43121438..43122057,2	Hela-S3	cervix:
16	chr1:113008897..113009443-chr1:113162104..113162760,2	MCF-7	breast:
17	chr1:112996718..113000080-chr1:113160996..113163127,3	K562	blood:
18	chr1:113160681..113163117-chr1:150458124..150460105,2	MCF-7	breast:
19	chr1:113159954..113164373-chr1:113192711..113196451,4	K562	blood:
20	chr1:112298302..112300134-chr1:113160714..113163318,3	MCF-7	breast:
21	chr1:113160723..113165170-chr1:113245654..113250392,12	K562	blood:
22	chr1:113160649..113163501-chr1:113258154..113260079,2	MCF-7	breast:
23	chr1:113157097..113164348-chr1:113214570..113220795,12	MCF-7	breast:
24	chr1:113156399..113165396-chr1:113241191..113253782,55	MCF-7	breast:
25	chr1:17231269..17231894-chr1:113162191..113162886,2	Hela-S3	cervix:
26	chr1:113003059..113010084-chr1:113159503..113164005,9	MCF-7	breast:
27	chr1:113162099..113162925-chr12:66563110..66563903,2	Hela-S3	cervix:
28	chr1:113160457..113163834-chr1:113216051..113218044,4	K562	blood:
29	chr1:113162187..113162713-chr1:201475946..201476502,2	Hela-S3	cervix:
30	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
31	chr1:113158395..113164969-chr1:113214433..113222934,24	MCF-7	breast:
32	chr1:113161963..113162630-chr7:100026036..100026682,2	NB4	blood:
33	chr1:113162339..113164666-chr17:59475031..59477488,2	MCF-7	breast:
34	chr1:113161754..113162505-chr10:90750781..90751305,2	Hela-S3	cervix:
35	chr1:113161720..113162463-chr10:101380776..101381707,2	Hela-S3	cervix:
36	chr1:113160231..113165111-chr1:113199772..113204361,6	K562	blood:
37	chr1:113160638..113164364-chr1:113256565..113260015,7	MCF-7	breast:
38	chr1:113160723..113165186-chr1:113170921..113177730,6	MCF-7	breast:
39	chr1:112934847..112940551-chr1:113160058..113165450,12	MCF-7	breast:
40	chr1:113160799..113166409-chr1:113215716..113220433,9	K562	blood:
41	chr1:113161757..113162713-chr16:46864244..46865084,2	Hela-S3	cervix:
42	chr1:113160402..113162739-chr1:113234192..113237024,2	K562	blood:
43	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:
44	chr1:113162051..113162904-chr1:113216304..113217427,3	MCF-7	breast:
45	chr1:113162194..113163025-chr1:156084431..156084953,2	Hela-S3	cervix:
46	chr1:113161699..113162604-chr17:74732949..74733754,2	Hela-S3	cervix:
47	chr1:113160602..113163896-chr1:113252357..113259247,7	K562	blood:
48	chr1:113160555..113166228-chr1:113255932..113262161,8	K562	blood:

No data

Variant related genes	Relation type
CAPZA1	TF binding region
ST7L	TF binding region
ENSG00000260475	Chromatin interaction
ENSG00000134245	Chromatin interaction
ENSG00000155380	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000087077	Chromatin interaction
ENSG00000107341	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000224536	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000107796	Chromatin interaction
ENSG00000143374	Chromatin interaction
ENSG00000026103	Chromatin interaction
ENSG00000134108	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000272426	Chromatin interaction
ENSG00000064703	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000159176	Chromatin interaction
ENSG00000092931	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000225075	Chromatin interaction
ENSG00000197852	Chromatin interaction
ENSG00000160789	Chromatin interaction
ENSG00000271810	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000033030	Chromatin interaction
ENSG00000159140	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000161547	Chromatin interaction
ENSG00000155957	Chromatin interaction
ENSG00000155330	Chromatin interaction
ENSG00000252750	Chromatin interaction
ENSG00000143079	Chromatin interaction
ENSG00000159131	Chromatin interaction
ENSG00000155366	Chromatin interaction
ENSG00000226419	Chromatin interaction
ENSG00000254458	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000238975	Chromatin interaction
ENSG00000235481	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10399919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102490	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes]
rs11102493	1.00[MEX][hapmap]
rs11102500	0.90[AFR][1000 genomes]
rs11102519	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102521	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175640	1.00[MEX][hapmap]
rs1175642	1.00[MEX][hapmap]
rs12060267	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069022	0.84[ASW][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs12069740	0.84[ASW][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073750	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12074157	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077330	0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080006	0.90[AFR][1000 genomes]
rs12082350	0.83[AFR][1000 genomes]
rs12085734	1.00[MEX][hapmap]
rs12091635	0.90[AFR][1000 genomes]
rs12094504	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs12095563	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030350	1.00[MEX][hapmap]
rs17030446	0.84[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes]
rs17030451	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs17030455	0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs17030475	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes]
rs17030592	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4424506	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57573777	1.00[AMR][1000 genomes]
rs58634778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59053530	1.00[AMR][1000 genomes]
rs59324334	0.85[AFR][1000 genomes]
rs61203550	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72982599	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72984503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72984509	1.00[AMR][1000 genomes]
rs72984515	1.00[AMR][1000 genomes]
rs72986505	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72986535	1.00[AMR][1000 genomes]
rs72993072	0.90[AFR][1000 genomes]
rs7542272	1.00[MEX][hapmap]
rs9919308	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 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	chr1:113159800-113164000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:113160000-113163400	Active TSS	Thymus	Thymus
3	chr1:113160000-113164400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:113160000-113165400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:113160200-113163600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:113160200-113163600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:113160400-113163200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:113160400-113163200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:113160400-113163800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr1:113160400-113163800	Active TSS	Primary T cells fromperipheralblood	blood
11	chr1:113160400-113163800	Active TSS	HSMMtube	muscle
12	chr1:113160400-113164000	Active TSS	Psoas Muscle	Psoas
13	chr1:113160400-113164000	Active TSS	A549	lung
14	chr1:113160400-113164600	Active TSS	K562	blood
15	chr1:113160600-113163000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:113160600-113163200	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr1:113160600-113163200	Active TSS	Right Ventricle	heart
18	chr1:113160600-113163200	Active TSS	HMEC	breast
19	chr1:113160600-113163400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr1:113160600-113163400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:113160600-113163400	Active TSS	Fetal Thymus	thymus
22	chr1:113160600-113163400	Active TSS	HSMM	muscle
23	chr1:113160600-113163600	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr1:113160600-113163600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:113160600-113163600	Active TSS	Colonic Mucosa	Colon
26	chr1:113160600-113166000	Active TSS	GM12878-XiMat	blood
27	chr1:113160800-113162800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:113160800-113163000	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr1:113160800-113163000	Active TSS	Brain Cingulate Gyrus	brain
30	chr1:113160800-113163200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:113160800-113163200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr1:113160800-113163200	Active TSS	Brain Angular Gyrus	brain
33	chr1:113160800-113163200	Active TSS	Fetal Stomach	stomach
34	chr1:113160800-113163200	Active TSS	Lung	lung
35	chr1:113160800-113163200	Active TSS	Pancreas	Pancrea
36	chr1:113160800-113163200	Active TSS	Osteobl	bone
37	chr1:113160800-113163400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:113160800-113163400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:113160800-113163400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:113160800-113163400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:113160800-113163400	Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr1:113160800-113163400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:113160800-113163400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:113160800-113163400	Active TSS	Fetal Brain Female	brain
45	chr1:113160800-113163400	Active TSS	Fetal Intestine Large	intestine
46	chr1:113160800-113163400	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr1:113160800-113163400	Active TSS	Fetal Muscle Trunk	muscle
48	chr1:113160800-113163400	Active TSS	Left Ventricle	heart
49	chr1:113160800-113163400	Active TSS	Stomach Mucosa	stomach
50	chr1:113160800-113163400	Active TSS	NHDF-Ad	bronchial

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