Variant report

Variant	rs6560019
Chromosome Location	chr9:72783971-72783972
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10119662	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10125617	0.83[JPT][hapmap]
rs10481740	0.81[ASN][1000 genomes]
rs10481741	0.81[ASN][1000 genomes]
rs1052684	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs10735583	0.81[ASN][1000 genomes]
rs10780811	0.81[ASN][1000 genomes]
rs10780923	0.81[ASN][1000 genomes]
rs10868646	0.87[AFR][1000 genomes]
rs10868720	0.83[JPT][hapmap]
rs10868752	0.85[ASN][1000 genomes]
rs10868757	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10868799	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs10868801	0.84[JPT][hapmap]
rs10868806	0.82[JPT][hapmap]
rs11142029	0.83[EUR][1000 genomes]
rs11142350	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1536956	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs1927106	0.81[ASN][1000 genomes]
rs1927115	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1927128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1927129	0.86[EUR][1000 genomes]
rs1927137	0.85[EUR][1000 genomes]
rs1927139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2026136	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs2148861	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2182736	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2182739	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs2209779	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2281935	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2309611	0.94[CEU][hapmap]
rs2309633	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2309642	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2309647	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2975890	0.81[ASN][1000 genomes]
rs3847321	0.84[ASN][1000 genomes]
rs3858107	0.83[ASN][1000 genomes]
rs4375070	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4744977	0.81[ASN][1000 genomes]
rs4744978	0.81[ASN][1000 genomes]
rs4745000	0.83[JPT][hapmap]
rs7021420	0.81[ASN][1000 genomes]
rs7027209	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7469211	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9650766	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72726800-72785200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:72741600-72789400	Weak transcription	Spleen	Spleen
3	chr9:72759600-72800000	Weak transcription	Right Ventricle	heart
4	chr9:72759800-72792200	Weak transcription	HMEC	breast
5	chr9:72760000-72785200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:72766200-72785200	Weak transcription	Left Ventricle	heart
7	chr9:72775200-72800000	Weak transcription	Esophagus	oesophagus
8	chr9:72775800-72785200	Weak transcription	Adipose Nuclei	Adipose
9	chr9:72776800-72791800	Weak transcription	Fetal Lung	lung
10	chr9:72777000-72792400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:72777200-72784800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:72777400-72789400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:72777800-72785200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:72777800-72785400	Weak transcription	Ovary	ovary
15	chr9:72777800-72800000	Weak transcription	Fetal Stomach	stomach
16	chr9:72778400-72785400	Weak transcription	Aorta	Aorta
17	chr9:72779200-72789600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:72779200-72792400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:72780400-72796000	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:72780400-72800000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:72780600-72785200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:72780600-72785200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr9:72780600-72785600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:72780600-72787600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:72780600-72791400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:72780600-72801400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr9:72780600-72803600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:72780800-72791600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:72781800-72784000	Enhancers	HepG2	liver
30	chr9:72782800-72784800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr9:72782800-72785000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:72783000-72792000	Strong transcription	HSMMtube	muscle
33	chr9:72783600-72784400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:72783600-72786200	Strong transcription	HSMM	muscle
35	chr9:72783600-72789800	Strong transcription	Colon Smooth Muscle	Colon
36	chr9:72783600-72792400	Weak transcription	Pancreas	Pancrea
37	chr9:72783600-72793600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:72783600-72794000	Strong transcription	Stomach Smooth Muscle	stomach
39	chr9:72783800-72786000	Strong transcription	NH-A	brain
40	chr9:72783800-72801600	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links