Variant report

Variant	rs1011095
Chromosome Location	chr4:56264941-56264942
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	FOXA1	chr4:56264652-56264957	HepG2	liver:	n/a	n/a
2	FOXA1	chr4:56264642-56264986	HepG2	liver:	n/a	n/a
3	MXI1	chr4:56260947-56266145	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr4:56264595-56264980	U87	brain:	n/a	n/a
5	FOS	chr4:56264209-56265894	MCF10A-Er-Src	breast:	n/a	n/a
6	JUND	chr4:56264366-56265013	K562	blood:	n/a	n/a
7	MYC	chr4:56264187-56265000	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr4:56264165-56265001	IMR90	lung:	n/a	chr4:56264368-56264379
9	FOXA2	chr4:56264664-56264947	HepG2	liver:	n/a	n/a
10	STAT3	chr4:56263026-56265466	MCF10A-Er-Src	breast:	n/a	chr4:56264390-56264401 chr4:56263633-56263641 chr4:56264742-56264753
11	POLR2A	chr4:56264702-56264974	SK-N-SH	brain:	n/a	n/a
12	ARID3A	chr4:56264297-56265424	HepG2	liver:	n/a	n/a
13	GATA1	chr4:56264211-56265348	PBDE	blood:	n/a	chr4:56264840-56264849
14	RCOR1	chr4:56264778-56265010	K562	blood:	n/a	n/a
15	POLR2A	chr4:56263945-56265097	U87	brain:	n/a	n/a
16	POLR2A	chr4:56261304-56265017	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr4:56261116-56266115	IMR90	lung:	n/a	n/a
18	MXI1	chr4:56261402-56265198	IMR90	lung:	n/a	n/a
19	TCF7L2	chr4:56264599-56265090	PANC-1	pancreas:	n/a	chr4:56264724-56264733 chr4:56264721-56264735 chr4:56264720-56264736 chr4:56264720-56264736
20	KAP1	chr4:56263744-56264951	HEK293	kidney:	n/a	chr4:56264742-56264750
21	FOS	chr4:56264766-56264984	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr4:56263918-56265146	U87	brain:	n/a	n/a
23	CUX1	chr4:56264372-56265037	K562	blood:	n/a	n/a
24	FOS	chr4:56264180-56265531	MCF10A-Er-Src	breast:	n/a	n/a
25	CHD1	chr4:56261060-56266047	IMR90	lung:	n/a	n/a
26	POLR2A	chr4:56264045-56265557	PBDE	blood:	n/a	n/a
27	MYC	chr4:56264221-56265284	MCF10A-Er-Src	breast:	n/a	n/a
28	FOXA1	chr4:56264614-56264949	HepG2	liver:	n/a	n/a
29	STAT3	chr4:56264173-56265531	MCF10A-Er-Src	breast:	n/a	chr4:56264390-56264401 chr4:56264742-56264753
30	ZNF384	chr4:56263693-56265212	K562	blood:	n/a	n/a
31	MAX	chr4:56264702-56264978	K562	blood:	n/a	n/a
32	STAT3	chr4:56264128-56265365	MCF10A-Er-Src	breast:	n/a	chr4:56264390-56264401 chr4:56264742-56264753
33	POLR2A	chr4:56264249-56265911	K562	blood:	n/a	n/a
34	STAT3	chr4:56264123-56265002	Hela-S3	cervix:	n/a	chr4:56264390-56264401 chr4:56264742-56264753
35	POLR2A	chr4:56264723-56264977	K562	blood:	n/a	n/a
36	FOS	chr4:56264233-56265510	MCF10A-Er-Src	breast:	n/a	n/a
37	TEAD4	chr4:56263787-56265060	K562	blood:	n/a	n/a
38	POLR2A	chr4:56261443-56265387	MCF10A-Er-Src	breast:	n/a	n/a
39	MXI1	chr4:56264517-56265001	K562	blood:	n/a	n/a
40	ARID3A	chr4:56264307-56265111	K562	blood:	n/a	n/a
41	FOXA2	chr4:56264589-56264954	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:56261651..56266514-chr4:56267808..56271520,10	MCF-7	breast:
2	chr4:56211148..56230966-chr4:56256626..56269458,54	MCF-7	breast:
3	chr4:56211096..56216124-chr4:56256262..56265067,20	K562	blood:
4	chr4:56211242..56218739-chr4:56258356..56267013,28	MCF-7	breast:
5	chr4:56211281..56215987-chr4:56257992..56268538,18	K562	blood:
6	chr4:56247536..56249762-chr4:56263632..56266279,3	K562	blood:
7	chr4:56216631..56219343-chr4:56262936..56265336,2	K562	blood:
8	chr17:46126036..46126788-chr4:56264311..56264974,2	Hela-S3	cervix:
9	chr4:56262170..56264152-chr4:56264363..56265916,3	K562	blood:
10	chr4:56216631..56219493-chr4:56263836..56266245,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRD5A3-4	chr4:56264559-56265055	NONHSAT096458

Variant related genes	Relation type
SRD5A3-AS1	TF binding region
TMEM165	TF binding region
ENSG00000251111	Chromatin interaction
ENSG00000128039	Chromatin interaction
ENSG00000249700	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000134851	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10002541	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10005989	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs10016506	0.86[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap]
rs10026692	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs11133376	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11133379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11133383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11133399	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1128141	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11726609	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11733864	0.84[AMR][1000 genomes]
rs11735267	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11931061	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11939815	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs11947476	0.81[AMR][1000 genomes]
rs11947623	0.81[AMR][1000 genomes]
rs13102385	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes]
rs13121235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13128582	0.81[AMR][1000 genomes]
rs1522106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1522111	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1873092	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap]
rs1965467	0.84[AMR][1000 genomes]
rs2177127	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2177129	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2412643	0.83[EUR][1000 genomes]
rs2412646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs2412663	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs28665088	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28726308	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2899037	0.89[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap]
rs3736544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs3736545	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3805147	1.00[CEU][hapmap]
rs3805154	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3817444	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap]
rs4580704	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs473005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs480479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4865010	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4865018	0.89[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs501679	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs564762	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs576779	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6554286	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6811520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6812042	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6815516	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6817267	0.81[AMR][1000 genomes]
rs6824955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6829182	0.96[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap]
rs6832769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs6837710	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6850524	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs6851838	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs6853192	0.96[CEU][hapmap]
rs726967	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7660054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7667849	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7668147	0.80[AMR][1000 genomes]
rs7673908	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs7684810	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs819271	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9312662	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9993675	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9997288	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 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	chr4:56261200-56265200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:56261400-56265000	Active TSS	H1 Cell Line	embryonic stem cell
3	chr4:56261400-56265200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:56261400-56265200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:56261400-56265200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr4:56261400-56265400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr4:56261400-56265400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr4:56261400-56265400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:56261400-56265400	Active TSS	Aorta	Aorta
10	chr4:56261400-56265400	Active TSS	Lung	lung
11	chr4:56261400-56265400	Active TSS	Psoas Muscle	Psoas
12	chr4:56261400-56265600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr4:56261400-56265600	Active TSS	HSMMtube	muscle
14	chr4:56261400-56266000	Active TSS	Right Atrium	heart
15	chr4:56261600-56265200	Active TSS	NHDF-Ad	bronchial
16	chr4:56261600-56265200	Active TSS	NHLF	lung
17	chr4:56261600-56265400	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr4:56261600-56265400	Active TSS	Pancreas	Pancrea
19	chr4:56261600-56265400	Active TSS	GM12878-XiMat	blood
20	chr4:56261600-56266000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:56262400-56265000	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr4:56262400-56265600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:56262600-56265200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:56262600-56265400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:56262800-56265000	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr4:56262800-56265000	Flanking Active TSS	Fetal Brain Male	brain
27	chr4:56262800-56265400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:56262800-56265600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr4:56262800-56266000	Transcr. at gene 5' and 3'	Dnd41	blood
30	chr4:56263200-56265200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr4:56263400-56265000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
32	chr4:56263400-56265800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
33	chr4:56263400-56265800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr4:56263400-56265800	Transcr. at gene 5' and 3'	NHEK	skin
35	chr4:56263400-56265800	Transcr. at gene 5' and 3'	Osteobl	bone
36	chr4:56263400-56266000	Transcr. at gene 5' and 3'	K562	blood
37	chr4:56263600-56265600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:56263600-56265800	Enhancers	Fetal Heart	heart
39	chr4:56263600-56266000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:56263600-56266000	Enhancers	Primary B cells from peripheral blood	blood
41	chr4:56263800-56265000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:56263800-56265000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr4:56263800-56265400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:56263800-56265600	Active TSS	Liver	Liver
45	chr4:56263800-56265800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr4:56263800-56266200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr4:56264000-56265000	Flanking Active TSS	Thymus	Thymus
48	chr4:56264000-56265000	Flanking Active TSS	HMEC	breast
49	chr4:56264000-56265200	Active TSS	Brain Substantia Nigra	brain
50	chr4:56264200-56265000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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