Variant report

Variant	rs1180099
Chromosome Location	chr9:72877558-72877559
allele	A/C
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	RUNX3	chr9:72877152-72877866	GM12878	blood:	n/a	n/a
3	STAT3	chr9:72877351-72877715	GM12878	blood:	n/a	n/a
4	BATF	chr9:72877297-72877637	GM12878	blood:	n/a	n/a
5	EP300	chr9:72877281-72877860	GM12878	blood:	n/a	n/a
6	CUX1	chr9:72877361-72878007	GM12878	blood:	n/a	n/a
7	RUNX3	chr9:72877249-72877698	GM12878	blood:	n/a	n/a
8	WRNIP1	chr9:72877482-72877566	GM12878	blood:	n/a	n/a
9	NFIC	chr9:72877145-72878106	GM12878	blood:	n/a	chr9:72877904-72877921 chr9:72877904-72877920
10	EBF1	chr9:72877328-72877622	GM12878	blood:	n/a	n/a
11	NFYB	chr9:72877166-72877630	GM12878	blood:	n/a	n/a
12	ATF2	chr9:72877254-72878068	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72874893..72877687-chr9:72912931..72914790,2	K562	blood:

Variant related genes	Relation type
SMC5-AS1	TF binding region

Extended variants
information (count: 140 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10116549	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10117899	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125454	0.83[EUR][1000 genomes]
rs10126027	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10780870	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780871	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780924	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs10868742	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868800	1.00[CHB][hapmap]
rs10868808	0.84[YRI][hapmap]
rs1112937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11141917	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142348	1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11142363	0.80[LWK][hapmap];0.91[YRI][hapmap]
rs11142364	1.00[CHB][hapmap]
rs11142365	0.95[EUR][1000 genomes]
rs11142367	0.95[YRI][hapmap]
rs11142368	0.90[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap]
rs11142370	0.91[YRI][hapmap]
rs11142372	1.00[CHB][hapmap]
rs11142373	0.80[LWK][hapmap];0.89[MEX][hapmap];0.92[YRI][hapmap]
rs11142375	0.88[ASN][1000 genomes]
rs11142377	1.00[CHB][hapmap]
rs11142379	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs11142380	0.95[EUR][1000 genomes]
rs11142381	0.95[EUR][1000 genomes]
rs11521805	1.00[CHB][hapmap]
rs1180079	0.83[AFR][1000 genomes]
rs1180081	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180082	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs1180083	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180087	0.89[AFR][1000 genomes]
rs1180088	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180089	1.00[CHB][hapmap]
rs1180091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180098	0.89[AFR][1000 genomes]
rs1180100	1.00[CHB][hapmap]
rs1180101	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs1180103	0.83[AFR][1000 genomes]
rs1180104	0.90[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs1180105	0.88[MEX][hapmap]
rs1180106	0.89[AFR][1000 genomes]
rs1180107	0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs1180110	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes]
rs1180111	0.97[EUR][1000 genomes]
rs1180112	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs1180113	1.00[CHB][hapmap]
rs1180117	0.80[LWK][hapmap];0.91[YRI][hapmap]
rs1180118	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs1180119	1.00[CHB][hapmap]
rs1180122	0.92[YRI][hapmap]
rs1180124	0.91[YRI][hapmap]
rs1180126	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs1180127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180128	0.83[AFR][1000 genomes]
rs1180133	0.92[YRI][hapmap]
rs11998951	0.89[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap]
rs12006212	0.80[LWK][hapmap];0.89[MEX][hapmap];0.92[YRI][hapmap]
rs12115787	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12156606	0.95[YRI][hapmap]
rs12349698	0.90[AMR][1000 genomes]
rs12377677	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12380844	0.95[YRI][hapmap]
rs17051515	0.80[ASN][1000 genomes]
rs17052678	1.00[CHB][hapmap]
rs17454349	0.80[ASN][1000 genomes]
rs17454433	0.80[ASN][1000 genomes]
rs17526808	0.80[ASN][1000 genomes]
rs1887451	0.83[EUR][1000 genomes]
rs1927094	1.00[CHB][hapmap]
rs1927096	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927100	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927101	0.80[ASN][1000 genomes]
rs1927118	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1927124	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927130	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927132	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927133	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927134	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927135	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927136	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1927144	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1927146	1.00[CHB][hapmap];0.83[YRI][hapmap]
rs1986067	0.89[ASN][1000 genomes]
rs2026137	0.96[YRI][hapmap]
rs2148857	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148859	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148863	0.83[EUR][1000 genomes]
rs2148866	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2148867	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182734	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182735	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182737	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182738	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182741	1.00[ASN][1000 genomes]
rs2309634	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309645	1.00[CHB][hapmap]
rs2479033	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2768643	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2768644	0.83[AFR][1000 genomes]
rs2768645	0.88[AFR][1000 genomes]
rs2768646	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2773362	0.83[AFR][1000 genomes]
rs2773363	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773366	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871293	0.92[YRI][hapmap]
rs4384045	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4449855	0.80[LWK][hapmap];0.89[MEX][hapmap];0.92[YRI][hapmap]
rs4744591	0.87[AFR][1000 genomes]
rs4744989	0.92[AMR][1000 genomes]
rs4744993	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744999	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5019539	0.80[ASN][1000 genomes]
rs6560015	0.80[ASN][1000 genomes]
rs6560016	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6560018	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66524845	0.92[ASN][1000 genomes]
rs66756859	1.00[ASN][1000 genomes]
rs68171482	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019147	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020447	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024117	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024812	0.80[ASN][1000 genomes]
rs7034322	0.90[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap]
rs7043171	1.00[CHB][hapmap]
rs7047789	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7853298	0.83[EUR][1000 genomes]
rs7858988	0.80[LWK][hapmap];0.89[MEX][hapmap];0.92[YRI][hapmap]
rs7860729	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7868564	0.87[AFR][1000 genomes]
rs7869429	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871674	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs943534	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943535	1.00[CHB][hapmap]
rs943536	0.80[LWK][hapmap];0.89[MEX][hapmap];0.92[YRI][hapmap]

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	chr9:72875000-72877600	Enhancers	Liver	Liver
4	chr9:72875000-72878000	Enhancers	Psoas Muscle	Psoas
5	chr9:72875000-72879200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:72875000-72879400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr9:72875000-72949800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:72875200-72877600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
9	chr9:72875200-72878600	Enhancers	Small Intestine	intestine
10	chr9:72875200-72901400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:72875400-72877600	Genic enhancers	NHEK	skin
12	chr9:72875400-72877800	Transcr. at gene 5' and 3'	Dnd41	blood
13	chr9:72875400-72879200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:72875400-72879400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:72875400-72906200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:72875600-72877600	Genic enhancers	A549	lung
17	chr9:72875600-72877800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:72875600-72877800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:72875600-72877800	Genic enhancers	K562	blood
20	chr9:72875600-72878600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr9:72875600-72878600	Enhancers	Colon Smooth Muscle	Colon
22	chr9:72875600-72879200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr9:72875800-72877600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:72875800-72877600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:72875800-72878000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr9:72875800-72878400	Enhancers	Fetal Brain Female	brain
27	chr9:72875800-72878600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr9:72875800-72878600	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr9:72875800-72878800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr9:72875800-72879200	Weak transcription	Fetal Kidney	kidney
31	chr9:72875800-72884200	Weak transcription	Lung	lung
32	chr9:72876000-72877800	Genic enhancers	HepG2	liver
33	chr9:72876000-72878200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr9:72876000-72878400	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr9:72876000-72878400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr9:72876000-72878600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr9:72876000-72879800	Weak transcription	Left Ventricle	heart
38	chr9:72876000-72882400	Weak transcription	Fetal Intestine Small	intestine
39	chr9:72876000-72882400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr9:72876000-72883200	Strong transcription	Placenta	Placenta
41	chr9:72876000-72887600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:72876000-72898200	Weak transcription	Fetal Brain Male	brain
43	chr9:72876000-72906200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:72876200-72877600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr9:72876200-72877600	Genic enhancers	Fetal Lung	lung
46	chr9:72876200-72877600	Genic enhancers	Osteobl	bone
47	chr9:72876200-72877800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:72876200-72878400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr9:72876200-72878800	Genic enhancers	HSMMtube	muscle
50	chr9:72876200-72879200	Weak transcription	Adipose Nuclei	Adipose

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