Variant report

Variant	rs6663339
Chromosome Location	chr1:180542325-180542326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180470660..180473288-chr1:180541631..180543834,2	MCF-7	breast:
2	chr1:180530731..180535452-chr1:180539258..180542430,4	K562	blood:
3	chr1:180541054..180543559-chr1:180545286..180546828,2	K562	blood:
4	chr1:180535652..180538329-chr1:180539867..180543816,3	K562	blood:

Variant related genes	Relation type
ENSG00000135847	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10494531	1.00[ASN][1000 genomes]
rs12028578	0.92[EUR][1000 genomes]
rs12073348	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12077656	1.00[CHB][hapmap]
rs12562357	0.90[CEU][hapmap];0.91[EUR][1000 genomes]
rs12723609	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12735662	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12754682	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16856420	1.00[CHB][hapmap]
rs17301118	1.00[ASN][1000 genomes]
rs17301132	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17373022	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17373133	1.00[ASN][1000 genomes]
rs3845400	1.00[ASN][1000 genomes]
rs3845401	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs67466592	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72720941	1.00[ASN][1000 genomes]
rs72720943	1.00[ASN][1000 genomes]
rs72720953	1.00[ASN][1000 genomes]
rs72720958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr1:180536200-180543200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:180538600-180543400	Weak transcription	Fetal Brain Female	brain
3	chr1:180539600-180546200	Weak transcription	Left Ventricle	heart
4	chr1:180540600-180543400	Weak transcription	Fetal Heart	heart
5	chr1:180540600-180543400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr1:180540800-180542800	Enhancers	Duodenum Mucosa	Duodenum
7	chr1:180540800-180543400	Enhancers	Pancreas	Pancrea
8	chr1:180540800-180543600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:180541200-180544000	Enhancers	HepG2	liver
10	chr1:180541400-180542600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr1:180541600-180542400	Enhancers	Fetal Intestine Large	intestine
12	chr1:180541600-180543600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:180541600-180549600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:180541800-180543400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:180541800-180544600	Enhancers	Fetal Intestine Small	intestine
16	chr1:180541800-180544800	Weak transcription	Right Ventricle	heart
17	chr1:180542000-180543000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:180542000-180543600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:180542000-180543800	Enhancers	Fetal Brain Male	brain
20	chr1:180542200-180543200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:180542200-180543200	Weak transcription	Stomach Mucosa	stomach
22	chr1:180542200-180543200	Weak transcription	K562	blood
23	chr1:180542200-180543400	Weak transcription	HMEC	breast
24	chr1:180542200-180543600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:180542200-180543600	Weak transcription	NHEK	skin

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