Variant report

Variant	rs233939
Chromosome Location	chr6:132319245-132319246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	6:132269655-132282174..6:132317980-132319790	H1-hESC	embryonic stem cell:	embryo
2	chr6:132316653..132319485-chr6:132330291..132332319,2	K562	blood:

Variant related genes	Relation type
ENSG00000118523	Chromatin interaction
ENSG00000227220	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1206719	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1206726	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs1206733	0.81[AFR][1000 genomes]
rs1206734	0.86[CHB][hapmap];0.83[JPT][hapmap];0.81[AFR][1000 genomes]
rs12527379	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs13437472	0.82[AFR][1000 genomes]
rs170881	0.89[ASN][1000 genomes]
rs173055	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1930999	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1931000	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2095252	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs233907	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233909	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs233910	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs233912	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233914	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs233915	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233916	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233918	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233920	0.88[ASN][1000 genomes]
rs233921	0.89[ASN][1000 genomes]
rs233922	0.89[ASN][1000 genomes]
rs233924	0.89[ASN][1000 genomes]
rs233926	0.89[ASN][1000 genomes]
rs233927	0.88[ASN][1000 genomes]
rs233933	0.85[ASN][1000 genomes]
rs233935	0.87[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs233936	0.81[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs233942	0.87[ASN][1000 genomes]
rs233943	0.89[ASN][1000 genomes]
rs233945	0.89[ASN][1000 genomes]
rs403374	0.85[ASN][1000 genomes]
rs412319	0.85[ASN][1000 genomes]
rs440883	0.85[ASN][1000 genomes]
rs693712	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9321322	0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv7968	chr6:131917172-132321099	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv470861	chr6:132291785-132351866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv886672	chr6:132299748-132349215	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv886673	chr6:132299748-132363507	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv427768	chr6:132300468-132398477	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv970350	chr6:132317890-132327515	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132303000-132320600	Weak transcription	Left Ventricle	heart
2	chr6:132304800-132320600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:132306200-132319800	Weak transcription	HSMM	muscle
4	chr6:132306200-132321400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:132317600-132324400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:132317800-132319800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:132317800-132320600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:132318000-132319400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr6:132318000-132319800	Enhancers	Fetal Intestine Large	intestine
10	chr6:132318000-132320600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:132318200-132319600	Enhancers	Fetal Intestine Small	intestine
12	chr6:132318200-132320000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr6:132318600-132320000	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr6:132318600-132320800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:132318800-132320000	Enhancers	A549	lung
16	chr6:132318800-132320800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:132318800-132324800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:132319000-132319400	Enhancers	Liver	Liver
19	chr6:132319000-132319400	Enhancers	Stomach Mucosa	stomach
20	chr6:132319200-132319800	Weak transcription	Aorta	Aorta
21	chr6:132319200-132320000	Weak transcription	Fetal Stomach	stomach
22	chr6:132319200-132320400	Enhancers	HepG2	liver
23	chr6:132319200-132320800	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links