Variant report

Variant	rs1180089
Chromosome Location	chr9:72869044-72869045
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72868706..72870705-chr9:73034414..73037199,2	K562	blood:
2	chr9:72868452..72871714-chr9:72871997..72874564,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268364	Chromatin interaction
ENSG00000198887	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

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];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs10868800	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[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];0.81[YRI][hapmap]
rs11142348	0.86[CEU][hapmap];0.95[EUR][1000 genomes]
rs11142364	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]
rs11142365	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11142372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[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];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[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];0.90[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];0.85[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	1.00[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];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180086	1.00[CHB][hapmap]
rs1180091	1.00[CHB][hapmap]
rs1180094	1.00[CHB][hapmap]
rs1180097	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180099	1.00[CHB][hapmap]
rs1180100	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]
rs1180110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1180111	0.89[AFR][1000 genomes]
rs1180113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];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];0.84[YRI][hapmap];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	1.00[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];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888155	0.81[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];1.00[YRI][hapmap];0.82[AFR][1000 genomes];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];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
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];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309646	0.85[AFR][1000 genomes];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]
rs2997683	0.84[GIH][hapmap]
rs3015215	0.84[GIH][hapmap]
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	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	1.00[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	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943532	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943533	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];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943540	0.82[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:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72845000-72870400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:72847400-72870800	Weak transcription	Pancreas	Pancrea
3	chr9:72855800-72870800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:72860600-72870800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:72865800-72869200	Weak transcription	Liver	Liver
6	chr9:72867600-72870800	Weak transcription	Brain Angular Gyrus	brain
7	chr9:72867800-72870200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr9:72868000-72870200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr9:72868000-72870800	Weak transcription	Brain Substantia Nigra	brain
10	chr9:72868000-72871200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:72868000-72872600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:72868200-72869800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:72868200-72870400	Weak transcription	K562	blood
14	chr9:72868400-72870600	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:72868400-72870600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr9:72868400-72870800	Weak transcription	Fetal Stomach	stomach
17	chr9:72868400-72871000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:72868600-72870400	Weak transcription	Small Intestine	intestine
19	chr9:72869000-72869200	Enhancers	HepG2	liver
20	chr9:72869000-72869400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:72869000-72869800	Enhancers	Muscle Satellite Cultured Cells	--

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