Variant report

Variant	rs13317815
Chromosome Location	chr3:23988685-23988686
allele	C/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	chr3:23988647-23989955	Hela-S3	cervix:	n/a	n/a
2	CHD1	chr3:23987669-23989094	H1-hESC	embryonic stem cell:	n/a	n/a
3	RFX5	chr3:23988280-23989331	K562	blood:	n/a	chr3:23988706-23988723
4	ARID3A	chr3:23988644-23989296	K562	blood:	n/a	n/a
5	MAX	chr3:23988632-23989179	K562	blood:	n/a	n/a
6	MAZ	chr3:23986016-23989986	IMR90	lung:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
7	POLR2A	chr3:23988626-23989318	H1-hESC	embryonic stem cell:	n/a	n/a
8	KAP1	chr3:23988333-23988954	K562	blood:	n/a	n/a
9	POLR2A	chr3:23985541-23990663	H1-hESC	embryonic stem cell:	n/a	n/a
10	NR2F2	chr3:23988625-23989867	K562	blood:	n/a	n/a
11	CEBPB	chr3:23988560-23989334	Hela-S3	cervix:	n/a	n/a
12	GATA2	chr3:23988670-23989350	HUVEC	blood vessel:	n/a	n/a
13	GATA3	chr3:23988635-23989444	SK-N-SH	brain:	n/a	n/a
14	NFIC	chr3:23988624-23989370	SK-N-SH	brain:	n/a	n/a
15	TEAD4	chr3:23988660-23989354	SK-N-SH	brain:	n/a	n/a
16	JUND	chr3:23988513-23989495	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr3:23988652-23989450	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:23986717-23989259	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:23988583-23989423	HUVEC	blood vessel:	n/a	n/a
20	MAFK	chr3:23988549-23989284	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:23986439-23989249	IMR90	lung:	n/a	n/a
22	POLR2A	chr3:23986455-23989330	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:23988282..23990131-chr3:24033697..24035885,2	MCF-7	breast:
2	chr3:23846531..23848270-chr3:23987055..23988984,2	MCF-7	breast:
3	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
4	chr3:23988541..23991177-chr3:24537846..24539360,2	K562	blood:
5	chr3:23988335..23991846-chr3:24002543..24006084,3	K562	blood:
6	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
7	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
NKIRAS1	TF binding region
ENSG00000197885	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000170142	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs10084748	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1037635	0.83[MEX][hapmap]
rs11129128	0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs13087250	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13316457	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13321439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13321440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533141	0.87[EUR][1000 genomes]
rs1567579	0.92[EUR][1000 genomes]
rs1567580	0.92[EUR][1000 genomes]
rs2360020	0.87[ASN][1000 genomes]
rs28524116	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34036067	0.83[EUR][1000 genomes]
rs34058540	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34082882	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34593533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34866549	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35136361	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35457462	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35755171	0.84[EUR][1000 genomes]
rs35755253	0.84[EUR][1000 genomes]
rs36063721	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36089963	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3762775	0.80[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs3811714	0.85[CHB][hapmap]
rs3935253	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4131404	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4132595	0.93[ASN][1000 genomes]
rs4300960	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4490300	0.80[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4602333	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4858096	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4858102	0.82[CHB][hapmap]
rs4858564	0.80[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59090179	0.83[ASN][1000 genomes]
rs6550808	0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs66609380	0.87[EUR][1000 genomes]
rs67002637	0.81[EUR][1000 genomes]
rs67465878	0.83[ASN][1000 genomes]
rs67606949	0.85[EUR][1000 genomes]
rs6770052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778577	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790140	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6791805	0.83[MEX][hapmap]
rs6803587	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71324126	0.87[EUR][1000 genomes]
rs72627028	0.80[ASN][1000 genomes]
rs72627029	0.80[ASN][1000 genomes]
rs72627030	0.80[ASN][1000 genomes]
rs72627031	0.80[ASN][1000 genomes]
rs72627032	0.80[ASN][1000 genomes]
rs72627033	0.80[ASN][1000 genomes]
rs72627034	0.80[ASN][1000 genomes]
rs72627035	0.80[ASN][1000 genomes]
rs72627036	0.80[ASN][1000 genomes]
rs72627037	0.80[ASN][1000 genomes]
rs72627038	0.80[ASN][1000 genomes]
rs72627039	0.80[ASN][1000 genomes]
rs72627040	0.80[ASN][1000 genomes]
rs72627043	0.80[ASN][1000 genomes]
rs72627044	0.87[ASN][1000 genomes]
rs72627046	0.87[ASN][1000 genomes]
rs72627047	0.83[ASN][1000 genomes]
rs72627048	0.83[ASN][1000 genomes]
rs72627049	0.83[ASN][1000 genomes]
rs72627050	0.83[ASN][1000 genomes]
rs72627051	0.87[ASN][1000 genomes]
rs72627052	0.87[ASN][1000 genomes]
rs72627053	0.87[ASN][1000 genomes]
rs72627055	0.87[ASN][1000 genomes]
rs72627056	0.87[ASN][1000 genomes]
rs72627057	0.87[ASN][1000 genomes]
rs72627058	0.87[ASN][1000 genomes]
rs72627059	0.87[ASN][1000 genomes]
rs72627060	0.87[ASN][1000 genomes]
rs72627061	0.87[ASN][1000 genomes]
rs72627062	0.87[ASN][1000 genomes]
rs72627063	0.87[ASN][1000 genomes]
rs72627064	0.87[ASN][1000 genomes]
rs72627065	0.87[ASN][1000 genomes]
rs72627067	0.87[ASN][1000 genomes]
rs72627068	0.87[ASN][1000 genomes]
rs72627069	0.87[ASN][1000 genomes]
rs72627070	0.87[ASN][1000 genomes]
rs72627071	0.87[ASN][1000 genomes]
rs72627072	0.87[ASN][1000 genomes]
rs72627073	0.87[ASN][1000 genomes]
rs72627074	0.87[ASN][1000 genomes]
rs72627075	0.87[ASN][1000 genomes]
rs72627076	0.87[ASN][1000 genomes]
rs72627078	0.86[ASN][1000 genomes]
rs72627079	0.87[ASN][1000 genomes]
rs72627080	0.87[ASN][1000 genomes]
rs72627081	0.87[ASN][1000 genomes]
rs72627082	0.87[ASN][1000 genomes]
rs72627083	0.87[ASN][1000 genomes]
rs72627084	0.87[ASN][1000 genomes]
rs72627085	0.87[ASN][1000 genomes]
rs72627086	0.87[ASN][1000 genomes]
rs72627087	0.87[ASN][1000 genomes]
rs72627088	0.87[ASN][1000 genomes]
rs72627089	0.87[ASN][1000 genomes]
rs72627090	0.87[ASN][1000 genomes]
rs72627091	0.90[ASN][1000 genomes]
rs72627094	0.92[AMR][1000 genomes]
rs72627096	0.97[ASN][1000 genomes]
rs72627097	0.97[ASN][1000 genomes]
rs72627098	0.97[ASN][1000 genomes]
rs72627099	0.97[ASN][1000 genomes]
rs72627100	0.90[ASN][1000 genomes]
rs72627101	0.90[ASN][1000 genomes]
rs72627102	0.90[ASN][1000 genomes]
rs72628103	0.90[ASN][1000 genomes]
rs72628104	0.90[ASN][1000 genomes]
rs72628105	0.90[ASN][1000 genomes]
rs72628106	0.90[ASN][1000 genomes]
rs72628107	0.90[ASN][1000 genomes]
rs72628108	0.90[ASN][1000 genomes]
rs72628109	0.90[ASN][1000 genomes]
rs72628111	0.90[ASN][1000 genomes]
rs72628112	0.87[ASN][1000 genomes]
rs72628113	0.87[ASN][1000 genomes]
rs72628114	0.87[ASN][1000 genomes]
rs72628115	0.87[ASN][1000 genomes]
rs72628116	0.87[ASN][1000 genomes]
rs72628119	0.83[ASN][1000 genomes]
rs72628123	0.83[ASN][1000 genomes]
rs72628124	0.83[ASN][1000 genomes]
rs72628126	0.87[ASN][1000 genomes]
rs73150266	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73150299	0.90[EUR][1000 genomes]
rs7611018	1.00[MEX][hapmap];0.81[TSI][hapmap]
rs954748	0.94[EUR][1000 genomes]
rs9809225	0.89[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs9812419	0.83[MEX][hapmap]
rs9812870	0.83[EUR][1000 genomes]
rs9817923	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853954	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9855481	0.80[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9859567	0.80[CEU][hapmap]
rs9863123	0.85[CHB][hapmap]
rs9863176	0.85[EUR][1000 genomes]
rs9875577	0.80[CEU][hapmap]
rs9882067	0.82[YRI][hapmap]
rs9883834	0.80[ASW][hapmap];0.89[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23985600-23988800	Active TSS	H9 Cell Line	embryonic stem cell
2	chr3:23985800-23988800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:23986000-23988800	Active TSS	Aorta	Aorta
4	chr3:23986000-23988800	Active TSS	Ovary	ovary
5	chr3:23986200-23988800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr3:23986200-23988800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:23986200-23988800	Active TSS	Stomach Smooth Muscle	stomach
8	chr3:23987800-23988800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
9	chr3:23987800-23988800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr3:23987800-23989000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:23987800-23989000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:23987800-23989000	Active TSS	Right Atrium	heart
13	chr3:23987800-23989000	Flanking Active TSS	Osteobl	bone
14	chr3:23987800-23989200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:23987800-23989200	Flanking Active TSS	NH-A	brain
16	chr3:23987800-23990000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr3:23987800-23991200	Enhancers	Fetal Heart	heart
18	chr3:23988000-23989000	Flanking Active TSS	HMEC	breast
19	chr3:23988000-23989000	Flanking Active TSS	HUVEC	blood vessel
20	chr3:23988000-23989000	Flanking Active TSS	NHEK	skin
21	chr3:23988000-23989000	Flanking Active TSS	NHLF	lung
22	chr3:23988000-23989200	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr3:23988000-23989200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr3:23988000-23989200	Flanking Active TSS	Hela-S3	cervix
25	chr3:23988000-23989400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:23988000-23989400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:23988000-23989400	Flanking Active TSS	Brain Hippocampus Middle	brain
28	chr3:23988000-23990000	Flanking Active TSS	K562	blood
29	chr3:23988000-23995000	Weak transcription	Spleen	Spleen
30	chr3:23988200-23988800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:23988200-23988800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:23988200-23988800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:23988200-23988800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:23988200-23988800	Weak transcription	Esophagus	oesophagus
35	chr3:23988200-23988800	Weak transcription	Pancreas	Pancrea
36	chr3:23988200-23989000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:23988200-23989000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr3:23988200-23989000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr3:23988200-23989000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr3:23988200-23989000	Flanking Active TSS	HepG2	liver
41	chr3:23988200-23989200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr3:23988200-23989200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr3:23988200-23989400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:23988200-23989400	Weak transcription	Gastric	stomach
45	chr3:23988200-23989400	Weak transcription	Lung	lung
46	chr3:23988200-23990000	Enhancers	Left Ventricle	heart
47	chr3:23988200-23990000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr3:23988200-23990400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:23988200-23991000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:23988200-23992200	Enhancers	Small Intestine	intestine

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