Variant report

Variant	rs41270596
Chromosome Location	chr6:28547283-28547284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28546789..28548794-chr6:28552409..28554551,3	K562	blood:
2	chr6:28547195..28548794-chr6:28553051..28555384,2	K562	blood:
3	chr6:28542784..28545360-chr6:28545429..28548690,3	MCF-7	breast:
4	chr6:28532871..28537837-chr6:28545273..28547393,5	K562	blood:
5	chr6:27862073..27865049-chr6:28546272..28548839,2	K562	blood:

Variant related genes	Relation type
ENSG00000232040	Chromatin interaction
ENSG00000246350	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs2079705	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28382590	0.90[EUR][1000 genomes]
rs28382595	0.90[EUR][1000 genomes]
rs28382599	0.90[EUR][1000 genomes]
rs28382602	0.88[EUR][1000 genomes]
rs28382603	0.90[EUR][1000 genomes]
rs28382609	0.88[EUR][1000 genomes]
rs28382614	0.90[EUR][1000 genomes]
rs28745594	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34757087	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34951544	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35062161	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35758328	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270579	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41270589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270593	0.86[EUR][1000 genomes]
rs4540253	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55965649	0.86[EUR][1000 genomes]
rs56043329	0.88[EUR][1000 genomes]
rs56975420	0.88[EUR][1000 genomes]
rs58078500	0.90[EUR][1000 genomes]
rs59653352	0.86[EUR][1000 genomes]
rs72844204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72844212	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72844218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72844220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72844224	1.00[ASN][1000 genomes]
rs72844225	1.00[ASN][1000 genomes]
rs72844226	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72844244	0.90[EUR][1000 genomes]
rs72850077	0.88[EUR][1000 genomes]
rs72854531	1.00[AFR][1000 genomes]
rs72854533	1.00[AFR][1000 genomes]
rs72854535	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72854536	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72854542	1.00[ASN][1000 genomes]
rs72854546	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72854553	1.00[ASN][1000 genomes]
rs72854556	1.00[AFR][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	chr6:28535000-28554000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:28536600-28553200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:28537200-28553200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:28537200-28554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:28537400-28553800	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:28538800-28553000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:28539400-28552800	Weak transcription	Fetal Intestine Large	intestine
10	chr6:28540000-28549200	Weak transcription	Ovary	ovary
11	chr6:28540000-28554000	Weak transcription	Gastric	stomach
12	chr6:28540600-28554200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:28541000-28554200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr6:28541400-28553200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:28541400-28554000	Weak transcription	Pancreas	Pancrea
16	chr6:28542200-28553200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:28542600-28553000	Weak transcription	Fetal Intestine Small	intestine
18	chr6:28543200-28547600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:28543600-28551400	Weak transcription	Fetal Brain Female	brain
20	chr6:28543600-28552400	Weak transcription	HepG2	liver
21	chr6:28543800-28553000	Weak transcription	Fetal Kidney	kidney
22	chr6:28543800-28553200	Weak transcription	Liver	Liver
23	chr6:28544000-28553200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:28544200-28552400	Weak transcription	Brain Germinal Matrix	brain
25	chr6:28544600-28552200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:28546200-28553000	Weak transcription	HMEC	breast
27	chr6:28547200-28551200	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links