Variant report

Variant	rs9855481
Chromosome Location	chr3:23989916-23989917
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	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
3	POLR2A	chr3:23988774-23992252	A549	lung:	n/a	n/a
4	POLR2A	chr3:23985541-23990663	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:23989541-23990574	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:23989629-23990518	HepG2	liver:	n/a	n/a

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

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10084748	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037635	1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs11129128	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129130	0.82[YRI][hapmap]
rs13070128	1.00[ASN][1000 genomes]
rs13087250	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316457	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317815	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]
rs13321439	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13321440	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1533141	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1567579	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567580	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28524116	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34036067	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34058540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34082882	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34593533	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34866549	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953164	1.00[ASN][1000 genomes]
rs35136361	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35457462	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35755171	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35755253	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36063721	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762775	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935253	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131404	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300960	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490300	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535169	1.00[ASN][1000 genomes]
rs4602333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858554	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4858556	1.00[ASN][1000 genomes]
rs4858564	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932805	1.00[ASN][1000 genomes]
rs6550808	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66609380	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67002637	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236598	1.00[ASN][1000 genomes]
rs67606949	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767005	1.00[ASN][1000 genomes]
rs6770052	0.86[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6775878	1.00[ASN][1000 genomes]
rs6776201	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6776568	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6778577	0.93[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6790140	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791805	1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs6803214	1.00[ASN][1000 genomes]
rs6803587	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71324126	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72627094	0.83[AMR][1000 genomes]
rs73150266	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150299	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610689	1.00[ASN][1000 genomes]
rs7610935	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7611018	1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs954748	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809225	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812419	1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs9812870	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9817923	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9853954	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859567	0.90[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs9863176	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875577	0.90[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882067	1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs9883834	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23987800-23990000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr3:23987800-23991200	Enhancers	Fetal Heart	heart
3	chr3:23988000-23990000	Flanking Active TSS	K562	blood
4	chr3:23988000-23995000	Weak transcription	Spleen	Spleen
5	chr3:23988200-23990000	Enhancers	Left Ventricle	heart
6	chr3:23988200-23990000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr3:23988200-23990400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:23988200-23991000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:23988200-23992200	Enhancers	Small Intestine	intestine
10	chr3:23988200-23992200	Enhancers	Stomach Mucosa	stomach
11	chr3:23988200-23993800	Enhancers	Brain Substantia Nigra	brain
12	chr3:23988200-24000600	Weak transcription	Fetal Brain Male	brain
13	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:23988400-23990000	Enhancers	Fetal Intestine Small	intestine
15	chr3:23988400-23990200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr3:23988400-23990400	Enhancers	Duodenum Mucosa	Duodenum
17	chr3:23988400-23990800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr3:23988400-23991600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr3:23988400-23991600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr3:23988400-23991800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:23988400-23992400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:23988400-23993600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr3:23988400-23995200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:23988400-23996000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:23988400-23996400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
28	chr3:23988600-23990600	Enhancers	Right Ventricle	heart
29	chr3:23988600-23991000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:23988600-23994000	Enhancers	Psoas Muscle	Psoas
31	chr3:23988600-23996000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr3:23988800-23990200	Enhancers	Rectal Smooth Muscle	rectum
33	chr3:23988800-23990600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:23988800-23991000	Weak transcription	Dnd41	blood
35	chr3:23988800-23991000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr3:23988800-23991200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:23988800-23991200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr3:23989000-23990000	Enhancers	HUVEC	blood vessel
39	chr3:23989000-23990200	Weak transcription	GM12878-XiMat	blood
40	chr3:23989000-23990400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:23989000-23990600	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr3:23989000-23991000	Weak transcription	Thymus	Thymus
43	chr3:23989000-23991200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr3:23989000-23991200	Weak transcription	Primary T cells from cord blood	blood
45	chr3:23989000-23991400	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr3:23989000-23991400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:23989000-23991400	Weak transcription	Fetal Intestine Large	intestine
48	chr3:23989000-23991400	Weak transcription	Fetal Stomach	stomach
49	chr3:23989000-23991600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:23989000-23991600	Enhancers	NHDF-Ad	bronchial

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