Variant report

Variant	rs10446730
Chromosome Location	chr4:120988934-120988935
allele	A/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	RUNX3	chr4:120988770-120989306	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:120987516-120988954	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:120986908-120989985	GM12891	blood:	n/a	n/a
4	POLR2A	chr4:120987337-120989347	GM19099	blood:	n/a	n/a
5	MBD4	chr4:120988073-120988951	HepG2	liver:	n/a	n/a
6	POLR2A	chr4:120987175-120989426	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:120987396-120989166	GM12892	blood:	n/a	n/a
8	POLR2A	chr4:120987270-120989178	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr4:120987152-120989112	PBDE	blood:	n/a	n/a
10	POLR2A	chr4:120987501-120989360	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:120987075-120989540	K562	blood:	n/a	n/a
12	GTF2F1	chr4:120987340-120989274	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr4:120987453-120989578	MCF10A-Er-Src	breast:	n/a	n/a
14	RELA	chr4:120987418-120988953	GM15510	blood:	n/a	n/a
15	MYC	chr4:120987219-120989379	K562	blood:	n/a	n/a
16	EP300	chr4:120987557-120989134	K562	blood:	n/a	chr4:120988036-120988052 chr4:120988608-120988615 chr4:120988776-120988790
17	RCOR1	chr4:120987491-120989172	HepG2	liver:	n/a	n/a
18	POLR2A	chr4:120987439-120989058	PANC-1	pancreas:	n/a	n/a
19	CEBPB	chr4:120988494-120988962	HepG2	liver:	n/a	chr4:120988777-120988786 chr4:120988777-120988786 chr4:120988775-120988788 chr4:120988775-120988788 chr4:120988775-120988786 chr4:120988777-120988786 chr4:120988777-120988786 chr4:120988775-120988788 chr4:120988777-120988788
20	POLR2A	chr4:120987349-120989466	GM18951	blood:	n/a	n/a
21	BHLHE40	chr4:120987397-120989312	K562	blood:	n/a	chr4:120987705-120987721
22	CEBPB	chr4:120987082-120988973	Hela-S3	cervix:	n/a	chr4:120988777-120988786 chr4:120988777-120988786 chr4:120988775-120988788 chr4:120988775-120988788 chr4:120988775-120988786 chr4:120988777-120988786 chr4:120988777-120988786 chr4:120987221-120987232 chr4:120988775-120988788 chr4:120987221-120987232 chr4:120988777-120988788
23	MYC	chr4:120986892-120989484	K562	blood:	n/a	n/a
24	ZNF143	chr4:120987490-120989113	GM12878	blood:	n/a	n/a
25	MXI1	chr4:120986904-120989097	IMR90	lung:	n/a	n/a
26	POLR2A	chr4:120988931-120989110	HUVEC	blood vessel:	n/a	n/a
27	MTA3	chr4:120987333-120988954	GM12878	blood:	n/a	n/a
28	CCNT2	chr4:120987557-120988945	K562	blood:	n/a	n/a
29	EP300	chr4:120987516-120989162	GM12878	blood:	n/a	chr4:120988036-120988052 chr4:120988608-120988615 chr4:120988776-120988790
30	MYBL2	chr4:120987540-120989014	HepG2	liver:	n/a	n/a
31	PML	chr4:120987500-120989102	K562	blood:	n/a	n/a
32	POLR2A	chr4:120987298-120989288	U87	brain:	n/a	n/a
33	POLR2A	chr4:120987163-120989871	K562	blood:	n/a	n/a
34	CEBPB	chr4:120988582-120988958	IMR90	lung:	n/a	chr4:120988777-120988786 chr4:120988777-120988786 chr4:120988775-120988788 chr4:120988775-120988788 chr4:120988775-120988786 chr4:120988777-120988786 chr4:120988777-120988786 chr4:120988775-120988788 chr4:120988777-120988788
35	CEBPB	chr4:120988465-120988999	A549	lung:	n/a	chr4:120988777-120988786 chr4:120988777-120988786 chr4:120988775-120988788 chr4:120988775-120988788 chr4:120988775-120988786 chr4:120988777-120988786 chr4:120988777-120988786 chr4:120988775-120988788 chr4:120988777-120988788
36	MXI1	chr4:120986183-120989454	SK-N-SH	brain:	n/a	n/a
37	RELA	chr4:120987261-120989116	GM10847	blood:	n/a	n/a
38	KAP1	chr4:120987512-120989283	HEK293	kidney:	n/a	n/a
39	RCOR1	chr4:120987396-120989670	K562	blood:	n/a	n/a
40	MAZ	chr4:120987233-120988959	K562	blood:	n/a	n/a
41	NR2F2	chr4:120987976-120989059	K562	blood:	n/a	n/a
42	POLR2A	chr4:120987349-120989227	GM19193	blood:	n/a	n/a
43	ZBTB7A	chr4:120988825-120989323	K562	blood:	n/a	n/a
44	POLR2A	chr4:120987326-120989395	K562	blood:	n/a	n/a
45	EBF1	chr4:120987639-120989081	GM12878	blood:	n/a	n/a
46	TCF7L2	chr4:120987738-120989004	HCT-116	colon:	n/a	n/a
47	POLR2A	chr4:120987270-120989356	GM12878	blood:	n/a	n/a
48	POLR2A	chr4:120987649-120989045	HepG2	liver:	n/a	n/a
49	POLR2A	chr4:120987111-120989454	GM18505	blood:	n/a	n/a
50	TAL1	chr4:120987479-120989045	K562	blood:	n/a	chr4:120988325-120988334

No.	Distal block	Cell Line	Cell type
1	chr4:120981267..120985179-chr4:120986108..120989816,4	MCF-7	breast:
2	chr4:120131923..120135922-chr4:120985229..120990455,5	K562	blood:
3	chr4:120987081..120989411-chr4:129732197..129734433,2	K562	blood:
4	chr4:120131661..120133788-chr4:120986266..120989312,3	K562	blood:
5	chr4:120220396..120223311-chr4:120987092..120990068,3	K562	blood:
6	chr4:119198442..119201160-chr4:120987880..120989467,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC110373.1-6	chr4:120988015-120991623	NONHSAT098115

Variant related genes	Relation type
MAD2L1	TF binding region
ENSG00000145390	Chromatin interaction
ENSG00000164109	Chromatin interaction
ENSG00000077684	Chromatin interaction
ENSG00000269893	Chromatin interaction
ENSG00000178636	Chromatin interaction
ENSG00000164096	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10446729	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11777	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61752609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61752610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6833927	1.00[AFR][1000 genomes]
rs72668809	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72668810	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72668812	1.00[AFR][1000 genomes]
rs72668814	1.00[AFR][1000 genomes]
rs72668820	1.00[AFR][1000 genomes]
rs72668821	1.00[AFR][1000 genomes]
rs72668824	1.00[AFR][1000 genomes]
rs72668829	1.00[AFR][1000 genomes]
rs72668830	1.00[AFR][1000 genomes]
rs72668835	1.00[AFR][1000 genomes]
rs72668836	1.00[AFR][1000 genomes]
rs72668838	1.00[AFR][1000 genomes]
rs72668839	1.00[AFR][1000 genomes]
rs72668840	1.00[AFR][1000 genomes]
rs72668859	1.00[AFR][1000 genomes]
rs72668868	1.00[AFR][1000 genomes]
rs72668872	1.00[AFR][1000 genomes]
rs72668874	1.00[AFR][1000 genomes]
rs72668875	1.00[AFR][1000 genomes]
rs72668898	1.00[AFR][1000 genomes]
rs72668899	1.00[AFR][1000 genomes]
rs72668902	1.00[AFR][1000 genomes]
rs72670409	1.00[AFR][1000 genomes]
rs72670410	1.00[AFR][1000 genomes]
rs72670412	1.00[AFR][1000 genomes]
rs72670414	1.00[AFR][1000 genomes]
rs72670415	1.00[AFR][1000 genomes]
rs72670416	1.00[AFR][1000 genomes]
rs72670420	1.00[AFR][1000 genomes]
rs72670421	1.00[AFR][1000 genomes]
rs72670425	1.00[AFR][1000 genomes]
rs72670427	1.00[AFR][1000 genomes]
rs72670428	1.00[AFR][1000 genomes]
rs72670431	1.00[AFR][1000 genomes]
rs72670444	1.00[AFR][1000 genomes]
rs72670447	1.00[AFR][1000 genomes]
rs72686517	1.00[AFR][1000 genomes]
rs72686518	1.00[AFR][1000 genomes]
rs72686524	1.00[AFR][1000 genomes]
rs72686526	1.00[AFR][1000 genomes]
rs72686529	1.00[AFR][1000 genomes]
rs72686533	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72686534	1.00[AFR][1000 genomes]
rs72686538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72686541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72686542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72686543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72686544	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72686546	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72686547	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72686550	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72686552	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7662162	1.00[AFR][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	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv1007641	chr4:120884220-121555889	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv537234	chr4:120884220-121555889	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120986000-120989000	Active TSS	A549	lung
2	chr4:120986000-120989200	Active TSS	K562	blood
3	chr4:120986400-120989000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:120986400-120989000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:120986400-120989000	Active TSS	NHDF-Ad	bronchial
6	chr4:120986400-120989200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:120986400-120989200	Active TSS	GM12878-XiMat	blood
8	chr4:120986400-120989400	Active TSS	H1 Cell Line	embryonic stem cell
9	chr4:120986600-120989000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr4:120986600-120989000	Active TSS	Thymus	Thymus
11	chr4:120986600-120989000	Active TSS	NHLF	lung
12	chr4:120986800-120989000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr4:120986800-120989400	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr4:120986800-120989800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr4:120987000-120989000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:120987000-120989000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:120987000-120989000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:120987000-120989000	Active TSS	Dnd41	blood
19	chr4:120987000-120989000	Active TSS	HSMM	muscle
20	chr4:120987000-120989600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:120987200-120989000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr4:120987200-120989000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:120987200-120989000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:120987200-120989000	Active TSS	Colonic Mucosa	Colon
25	chr4:120987200-120989000	Active TSS	HSMMtube	muscle
26	chr4:120987200-120989200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr4:120987400-120989000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:120987400-120989000	Active TSS	Colon Smooth Muscle	Colon
29	chr4:120987400-120989000	Active TSS	Lung	lung
30	chr4:120987400-120989200	Active TSS	Left Ventricle	heart
31	chr4:120987400-120989200	Active TSS	Right Atrium	heart
32	chr4:120987600-120989000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:120987600-120989000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:120987600-120989000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr4:120987600-120989000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr4:120987600-120989000	Active TSS	Brain Angular Gyrus	brain
37	chr4:120987600-120989000	Active TSS	Brain Anterior Caudate	brain
38	chr4:120987600-120989000	Active TSS	Brain Substantia Nigra	brain
39	chr4:120987600-120989000	Active TSS	Fetal Brain Female	brain
40	chr4:120987600-120989000	Active TSS	Psoas Muscle	Psoas
41	chr4:120987600-120989200	Active TSS	Aorta	Aorta
42	chr4:120987600-120989200	Active TSS	Right Ventricle	heart
43	chr4:120987800-120989000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr4:120987800-120989000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr4:120987800-120989000	Active TSS	Duodenum Mucosa	Duodenum
46	chr4:120987800-120989000	Active TSS	Pancreas	Pancrea
47	chr4:120987800-120989000	Active TSS	Stomach Mucosa	stomach
48	chr4:120988000-120989000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:120988000-120989000	Active TSS	Liver	Liver
50	chr4:120988000-120989000	Active TSS	Fetal Muscle Trunk	muscle

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