Variant report

Variant	rs1180109
Chromosome Location	chr9:72885267-72885268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:72872699..72874574-chr9:72884365..72888295,3	MCF-7	breast:
2	chr9:72884845..72889230-chr9:72890104..72893767,5	K562	blood:
3	chr9:72873820..72877013-chr9:72882771..72886042,3	K562	blood:

Variant related genes	Relation type
ENSG00000268364	Chromatin interaction
ENSG00000198887	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

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];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1104709	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11142141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11142346	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[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];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11793851	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11794396	0.84[AMR][1000 genomes]
rs1180085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1180090	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1180093	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1180095	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1180116	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];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12005243	0.84[AMR][1000 genomes]
rs12338030	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12343885	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12346675	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12352944	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12684881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2148856	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2183361	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4744593	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58704591	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62570318	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7019433	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7023586	0.84[AMR][1000 genomes]
rs7028657	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72712267	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72712271	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72712284	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7847861	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7849942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7868421	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7873075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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:125 , 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	chr9:72876000-72887600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:72876000-72898200	Weak transcription	Fetal Brain Male	brain
6	chr9:72876000-72906200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:72876400-72886200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:72876400-72886600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr9:72876400-72889200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:72876400-72916800	Weak transcription	Colonic Mucosa	Colon
11	chr9:72876400-72939400	Weak transcription	Spleen	Spleen
12	chr9:72876400-72942600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:72876400-72955200	Weak transcription	Stomach Mucosa	stomach
14	chr9:72876600-72885800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:72876600-72888200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr9:72876800-72900200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:72877000-72886000	Strong transcription	Fetal Thymus	thymus
18	chr9:72877000-72895400	Weak transcription	Right Ventricle	heart
19	chr9:72877000-72904800	Weak transcription	Brain Germinal Matrix	brain
20	chr9:72877000-72939800	Weak transcription	Gastric	stomach
21	chr9:72877000-72942800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:72877600-72909600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr9:72877600-72935800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:72877800-72887200	Weak transcription	Aorta	Aorta
25	chr9:72877800-72888000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:72877800-72892000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:72878000-72885800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:72878000-72887800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr9:72878400-72895000	Weak transcription	Fetal Brain Female	brain
30	chr9:72878600-72885400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr9:72878600-72889800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr9:72878600-72899600	Weak transcription	Fetal Heart	heart
33	chr9:72878600-72899800	Weak transcription	Small Intestine	intestine
34	chr9:72878600-72902400	Weak transcription	Brain Angular Gyrus	brain
35	chr9:72878600-72937600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr9:72878800-72885600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:72878800-72885600	Strong transcription	HUVEC	blood vessel
38	chr9:72878800-72887600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:72878800-72887800	Strong transcription	HSMM	muscle
40	chr9:72879000-72885400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:72879000-72885600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr9:72879000-72898600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr9:72879200-72885400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr9:72879200-72885400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr9:72879200-72885400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:72879200-72885400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr9:72879200-72885400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr9:72879200-72885400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr9:72879200-72885400	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr9:72879200-72885400	Strong transcription	Liver	Liver

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