Variant report

Variant	rs1180116
Chromosome Location	chr9:72897434-72897435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:72873053..72875021-chr9:72897295..72898936,2	MCF-7	breast:
2	chr9:72892928..72895718-chr9:72895750..72898961,3	K562	blood:
3	chr9:72897081..72899736-chr9:72903507..72905906,2	K562	blood:
4	chr9:72890363..72893798-chr9:72895489..72899233,4	K562	blood:

Variant related genes	Relation type
ENSG00000198887	Chromatin interaction
ENSG00000268364	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10868798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1104709	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11142141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11142346	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11142355	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];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793851	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1180090	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1180093	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1180095	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1180109	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];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1180131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338030	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12346675	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12684881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2183361	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4744593	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58704591	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62570318	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7019433	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7028657	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72712267	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72712271	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72712284	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7847861	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7849942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7868421	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7873075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1049132	chr9:72895382-73005897	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 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	chr9:72875000-72949800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:72875200-72901400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:72875400-72906200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:72876000-72898200	Weak transcription	Fetal Brain Male	brain
5	chr9:72876000-72906200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:72876400-72916800	Weak transcription	Colonic Mucosa	Colon
7	chr9:72876400-72939400	Weak transcription	Spleen	Spleen
8	chr9:72876400-72942600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:72876400-72955200	Weak transcription	Stomach Mucosa	stomach
10	chr9:72876800-72900200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:72877000-72904800	Weak transcription	Brain Germinal Matrix	brain
12	chr9:72877000-72939800	Weak transcription	Gastric	stomach
13	chr9:72877000-72942800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:72877600-72909600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:72877600-72935800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:72878600-72899600	Weak transcription	Fetal Heart	heart
17	chr9:72878600-72899800	Weak transcription	Small Intestine	intestine
18	chr9:72878600-72902400	Weak transcription	Brain Angular Gyrus	brain
19	chr9:72878600-72937600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr9:72879000-72898600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:72880000-72939400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr9:72880200-72906200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr9:72880400-72900200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:72881000-72905000	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:72881000-72905000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr9:72882800-72899800	Weak transcription	Ovary	ovary
27	chr9:72882800-72906000	Weak transcription	K562	blood
28	chr9:72883200-72899800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:72884600-72899800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr9:72885400-72916800	Weak transcription	Esophagus	oesophagus
31	chr9:72885800-72899800	Weak transcription	Thymus	Thymus
32	chr9:72885800-72900000	Weak transcription	Lung	lung
33	chr9:72887600-72906200	Weak transcription	Psoas Muscle	Psoas
34	chr9:72887600-72916800	Weak transcription	Aorta	Aorta
35	chr9:72888800-72898600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:72889400-72904200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:72890000-72905800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:72890400-72898000	Weak transcription	Fetal Intestine Small	intestine
39	chr9:72890400-72904800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:72891000-72905000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:72891000-72908800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr9:72891000-72911000	Strong transcription	HSMM	muscle
43	chr9:72891000-72923400	Strong transcription	Dnd41	blood
44	chr9:72891200-72907400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr9:72891400-72948200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr9:72891600-72899800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr9:72891600-72902400	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr9:72891600-72905200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr9:72891800-72900800	Strong transcription	HMEC	breast
50	chr9:72892600-72898200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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