Variant report

Variant	rs55873641
Chromosome Location	chr6:80313299-80313300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:80311176..80314030-chr6:80317329..80319854,3	MCF-7	breast:
2	chr6:80313208..80315896-chr6:80339700..80342572,2	K562	blood:
3	chr6:80313081..80315712-chr6:80421227..80423737,2	K562	blood:
4	chr6:80313064..80315190-chr6:80363540..80365628,2	K562	blood:

Variant related genes	Relation type
ENSG00000198478	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1504368	0.95[AFR][1000 genomes]
rs62413401	0.81[AFR][1000 genomes]
rs62413414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62413416	1.00[AFR][1000 genomes]
rs6917186	1.00[AFR][1000 genomes]
rs6920332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934060	1.00[AFR][1000 genomes]
rs6939569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73747413	1.00[AFR][1000 genomes]
rs73750727	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv830707	chr6:80134625-80325171	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1029259	chr6:80142754-80340332	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1018318	chr6:80241029-80465282	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv886304	chr6:80294265-80355973	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80298600-80324200	Weak transcription	Right Ventricle	heart
2	chr6:80307200-80314600	Weak transcription	Small Intestine	intestine
3	chr6:80310000-80314200	Weak transcription	Fetal Heart	heart
4	chr6:80310200-80314000	Enhancers	K562	blood
5	chr6:80310400-80314600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:80310400-80315800	Weak transcription	Gastric	stomach
7	chr6:80310400-80315800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr6:80310400-80317800	Weak transcription	Colonic Mucosa	Colon
9	chr6:80310600-80319200	Weak transcription	Psoas Muscle	Psoas
10	chr6:80310800-80314400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:80311000-80315800	Weak transcription	Hela-S3	cervix
12	chr6:80311000-80324400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:80311200-80313600	Weak transcription	HepG2	liver
14	chr6:80311200-80313800	Weak transcription	Fetal Intestine Large	intestine
15	chr6:80311200-80314000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr6:80311200-80314000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:80311200-80314000	Weak transcription	HMEC	breast
18	chr6:80311200-80314200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:80311200-80314200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:80311200-80315800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:80311200-80317200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:80311200-80324400	Weak transcription	Pancreas	Pancrea
23	chr6:80311400-80314000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:80311400-80314000	Weak transcription	Osteobl	bone
25	chr6:80311400-80315800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:80312200-80313400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr6:80312200-80313400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:80312200-80314800	Weak transcription	Stomach Mucosa	stomach
29	chr6:80312200-80319200	Enhancers	HSMM	muscle
30	chr6:80312400-80313400	Enhancers	Fetal Brain Female	brain
31	chr6:80312400-80313600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:80312400-80314000	Weak transcription	Fetal Intestine Small	intestine
33	chr6:80312600-80314600	Enhancers	HSMMtube	muscle
34	chr6:80312600-80315400	Enhancers	NH-A	brain
35	chr6:80312600-80316600	Weak transcription	Fetal Kidney	kidney
36	chr6:80312800-80316200	Weak transcription	Brain Angular Gyrus	brain
37	chr6:80313000-80316800	Weak transcription	Brain Anterior Caudate	brain
38	chr6:80313200-80314800	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links