Variant report

Variant	rs41270593
Chromosome Location	chr6:28543089-28543090
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28543041..28546521-chr6:28553899..28555966,3	K562	blood:
2	chr6:28535055..28538009-chr6:28541570..28543876,2	K562	blood:
3	chr6:28537910..28539578-chr6:28542732..28545368,2	MCF-7	breast:
4	chr6:28542784..28545360-chr6:28545429..28548690,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246350	Chromatin interaction
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs2394101	0.80[EUR][1000 genomes]
rs28382590	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382595	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382599	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382602	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382603	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382609	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382614	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28745594	0.95[EUR][1000 genomes]
rs34757087	0.95[EUR][1000 genomes]
rs34951544	0.95[EUR][1000 genomes]
rs35062161	0.95[EUR][1000 genomes]
rs35758328	0.95[EUR][1000 genomes]
rs41270579	0.80[EUR][1000 genomes]
rs41270596	0.86[EUR][1000 genomes]
rs4540253	0.80[EUR][1000 genomes]
rs55920503	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55965649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56043329	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56975420	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58078500	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59653352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72844212	0.80[EUR][1000 genomes]
rs72844223	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72844224	0.82[EUR][1000 genomes]
rs72844225	0.82[EUR][1000 genomes]
rs72844226	0.82[EUR][1000 genomes]
rs72844244	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850077	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850094	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854542	0.80[EUR][1000 genomes]
rs72854546	0.80[EUR][1000 genomes]
rs72854553	0.80[EUR][1000 genomes]
rs72854556	0.80[EUR][1000 genomes]
rs7770236	0.80[EUR][1000 genomes];1.00[ASN][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:27 , 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	chr6:28537200-28543800	Weak transcription	GM12878-XiMat	blood
7	chr6:28537200-28553200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:28537200-28554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:28537400-28553800	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:28538800-28553000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:28539400-28552800	Weak transcription	Fetal Intestine Large	intestine
12	chr6:28540000-28543200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:28540000-28549200	Weak transcription	Ovary	ovary
14	chr6:28540000-28554000	Weak transcription	Gastric	stomach
15	chr6:28540600-28544000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:28540600-28554200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:28540800-28543600	Strong transcription	Fetal Brain Female	brain
18	chr6:28541000-28554200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:28541200-28544200	Strong transcription	Brain Germinal Matrix	brain
20	chr6:28541400-28553200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:28541400-28554000	Weak transcription	Pancreas	Pancrea
22	chr6:28541600-28543800	Strong transcription	K562	blood
23	chr6:28542000-28543800	Strong transcription	Fetal Kidney	kidney
24	chr6:28542200-28544600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:28542200-28553200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:28542600-28553000	Weak transcription	Fetal Intestine Small	intestine
27	chr6:28542800-28543600	Strong transcription	HepG2	liver

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