Variant report

Variant	rs73402995
Chromosome Location	chr6:28542104-28542105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28535055..28538009-chr6:28541570..28543876,2	K562	blood:
2	chr6:28540275..28543041-chr6:28557463..28560801,3	K562	blood:

Variant related genes	Relation type
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1015810	0.86[ASN][1000 genomes]
rs11962141	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964748	1.00[EUR][1000 genomes]
rs11966949	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968771	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11969304	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11970404	0.86[ASN][1000 genomes]
rs2078422	0.86[ASN][1000 genomes]
rs2159274	1.00[ASN][1000 genomes]
rs2531802	0.86[ASN][1000 genomes]
rs2531812	1.00[ASN][1000 genomes]
rs2531819	0.86[ASN][1000 genomes]
rs28382592	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2859349	0.86[ASN][1000 genomes]
rs2859350	0.86[ASN][1000 genomes]
rs2859354	0.86[ASN][1000 genomes]
rs2859371	1.00[ASN][1000 genomes]
rs2859376	1.00[ASN][1000 genomes]
rs2859377	1.00[ASN][1000 genomes]
rs2859378	1.00[ASN][1000 genomes]
rs385908	0.86[ASN][1000 genomes]
rs400987	0.86[ASN][1000 genomes]
rs403774	0.86[ASN][1000 genomes]
rs423118	0.86[ASN][1000 genomes]
rs57083092	1.00[EUR][1000 genomes]
rs57147168	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58945456	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59457415	0.86[ASN][1000 genomes]
rs60137363	1.00[ASN][1000 genomes]
rs61540948	0.86[ASN][1000 genomes]
rs6923104	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73391136	0.86[ASN][1000 genomes]
rs73391164	0.86[ASN][1000 genomes]
rs73391166	0.86[ASN][1000 genomes]
rs73391169	0.86[ASN][1000 genomes]
rs73403142	0.86[ASN][1000 genomes]
rs73404956	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73404986	0.91[EUR][1000 genomes]
rs73405002	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407126	0.86[ASN][1000 genomes]
rs73409118	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73409123	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73409134	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7742658	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751604	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28531800-28553200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:28532000-28552600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:28534400-28543200	Weak transcription	Liver	Liver
4	chr6:28535000-28554000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:28536600-28553200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:28537200-28542200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:28537200-28543800	Weak transcription	GM12878-XiMat	blood
8	chr6:28537200-28553200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:28537200-28554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:28537400-28553800	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:28538800-28553000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:28539400-28552800	Weak transcription	Fetal Intestine Large	intestine
13	chr6:28540000-28543200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:28540000-28549200	Weak transcription	Ovary	ovary
15	chr6:28540000-28554000	Weak transcription	Gastric	stomach
16	chr6:28540600-28544000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:28540600-28554200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:28540800-28542800	Weak transcription	HepG2	liver
19	chr6:28540800-28543600	Strong transcription	Fetal Brain Female	brain
20	chr6:28541000-28554200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:28541200-28544200	Strong transcription	Brain Germinal Matrix	brain
22	chr6:28541400-28553200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:28541400-28554000	Weak transcription	Pancreas	Pancrea
24	chr6:28541600-28543800	Strong transcription	K562	blood
25	chr6:28542000-28543800	Strong transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links