Variant report

Variant	rs1180100
Chromosome Location	chr9:72877938-72877939
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	RELA	chr9:72877084-72878130	GM12878	blood:	n/a	n/a
2	EGR1	chr9:72877757-72877961	GM12878	blood:	n/a	n/a
3	CEBPB	chr9:72877872-72878671	IMR90	lung:	n/a	chr9:72878026-72878037 chr9:72878279-72878292
4	SPI1	chr9:72877826-72878090	GM12891	blood:	n/a	n/a
5	CUX1	chr9:72877361-72878007	GM12878	blood:	n/a	n/a
6	NFIC	chr9:72877145-72878106	GM12878	blood:	n/a	chr9:72877904-72877921 chr9:72877904-72877920
7	ZNF384	chr9:72877744-72878055	GM12878	blood:	n/a	n/a
8	CEBPB	chr9:72877869-72878192	HepG2	liver:	n/a	chr9:72878026-72878037
9	ATF2	chr9:72877254-72878068	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SMC5-AS1	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10114223	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735584	0.81[AMR][1000 genomes]
rs10780924	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs10868800	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10868810	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112937	1.00[CHB][hapmap]
rs11142348	0.86[CEU][hapmap];0.95[EUR][1000 genomes]
rs11142364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142365	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11142372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142375	0.91[EUR][1000 genomes]
rs11142377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142379	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs11142380	1.00[ASN][1000 genomes]
rs11142381	1.00[ASN][1000 genomes]
rs11521805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11795149	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180080	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180082	1.00[CHB][hapmap]
rs1180084	1.00[CEU][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180086	1.00[CHB][hapmap]
rs1180089	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180091	1.00[CHB][hapmap]
rs1180094	1.00[CHB][hapmap]
rs1180097	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180099	1.00[CHB][hapmap]
rs1180110	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1180111	0.91[AFR][1000 genomes]
rs1180113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180127	1.00[CHB][hapmap]
rs1180134	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1183311	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11999862	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888155	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927097	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927108	0.81[AMR][1000 genomes]
rs1927109	0.81[AMR][1000 genomes]
rs1927112	0.87[AMR][1000 genomes]
rs1927114	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1927123	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927138	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927140	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927141	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927145	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927148	0.81[YRI][hapmap]
rs2148854	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148855	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182733	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182735	1.00[CHB][hapmap]
rs2209781	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2225128	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309601	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2309637	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309641	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309644	1.00[CHB][hapmap]
rs2309645	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309646	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871297	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744587	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744985	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66524845	0.91[EUR][1000 genomes]
rs66756859	0.95[EUR][1000 genomes]
rs7020575	0.86[EUR][1000 genomes]
rs7042675	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043171	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs7047789	1.00[CHB][hapmap]
rs72712293	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72712300	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341691	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848955	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7865289	0.86[EUR][1000 genomes]
rs9410662	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943532	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943533	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943535	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription 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	66 gene(s)	inside rSNPs	diseases
2	nsv831615	chr9:72852705-73019692	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers 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	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72874800-72878600	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr9:72874800-72879200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:72875000-72878000	Enhancers	Psoas Muscle	Psoas
4	chr9:72875000-72879200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:72875000-72879400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr9:72875000-72949800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:72875200-72878600	Enhancers	Small Intestine	intestine
8	chr9:72875200-72901400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:72875400-72879200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr9:72875400-72879400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:72875400-72906200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:72875600-72878600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr9:72875600-72878600	Enhancers	Colon Smooth Muscle	Colon
14	chr9:72875600-72879200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr9:72875800-72878000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr9:72875800-72878400	Enhancers	Fetal Brain Female	brain
17	chr9:72875800-72878600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr9:72875800-72878600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr9:72875800-72878800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:72875800-72879200	Weak transcription	Fetal Kidney	kidney
21	chr9:72875800-72884200	Weak transcription	Lung	lung
22	chr9:72876000-72878200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr9:72876000-72878400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr9:72876000-72878400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:72876000-72878600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr9:72876000-72879800	Weak transcription	Left Ventricle	heart
27	chr9:72876000-72882400	Weak transcription	Fetal Intestine Small	intestine
28	chr9:72876000-72882400	Strong transcription	Fetal Muscle Trunk	muscle
29	chr9:72876000-72883200	Strong transcription	Placenta	Placenta
30	chr9:72876000-72887600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:72876000-72898200	Weak transcription	Fetal Brain Male	brain
32	chr9:72876000-72906200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:72876200-72878400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:72876200-72878800	Genic enhancers	HSMMtube	muscle
35	chr9:72876200-72879200	Weak transcription	Adipose Nuclei	Adipose
36	chr9:72876200-72880200	Strong transcription	Primary hematopoietic stem cells	blood
37	chr9:72876400-72878200	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr9:72876400-72878600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr9:72876400-72879000	Weak transcription	Right Atrium	heart
40	chr9:72876400-72879200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr9:72876400-72879200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:72876400-72879400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr9:72876400-72879600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:72876400-72879800	Weak transcription	Pancreas	Pancrea
45	chr9:72876400-72880400	Strong transcription	Fetal Intestine Large	intestine
46	chr9:72876400-72884200	Weak transcription	Esophagus	oesophagus
47	chr9:72876400-72884200	Weak transcription	Fetal Stomach	stomach
48	chr9:72876400-72886200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr9:72876400-72886600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr9:72876400-72889200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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