Variant report

Variant	rs6105560
Chromosome Location	chr20:16248193-16248194
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	chr20:16241933..16245769-chr20:16247318..16250085,3	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10485549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10485550	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11907241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11908227	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11908242	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11908381	0.87[AFR][1000 genomes]
rs16997595	1.00[JPT][hapmap]
rs17730831	1.00[ASN][1000 genomes]
rs17730901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17731020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144896	0.82[CHB][hapmap]
rs3848791	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848792	1.00[ASN][1000 genomes]
rs3848793	1.00[ASN][1000 genomes]
rs4052895	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276366	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4287828	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4416282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814466	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814467	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57988134	1.00[ASN][1000 genomes]
rs6105561	1.00[ASN][1000 genomes]
rs6105562	1.00[ASN][1000 genomes]
rs6105564	1.00[CHB][hapmap]
rs6110998	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6110999	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6111001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111007	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111008	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111012	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6111025	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs718610	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs878582	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs878583	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];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	nsv833930	chr20:16134347-16302763	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv519621	chr20:16236837-16248453	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv516591	chr20:16238023-16248453	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv3449914	chr20:16247143-16248367	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16242400-16275000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr20:16244800-16253400	Weak transcription	Ovary	ovary
3	chr20:16245600-16248200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:16246600-16253200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr20:16247200-16248600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr20:16247200-16248600	ZNF genes & repeats	Fetal Stomach	stomach
7	chr20:16247200-16249000	ZNF genes & repeats	Aorta	Aorta
8	chr20:16247400-16248400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr20:16247400-16248400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr20:16247400-16248600	Strong transcription	Stomach Smooth Muscle	stomach
11	chr20:16247400-16253600	Weak transcription	Gastric	stomach
12	chr20:16247600-16253200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr20:16247600-16290800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr20:16248000-16248200	ZNF genes & repeats	Fetal Intestine Small	intestine
15	chr20:16248000-16248400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr20:16248000-16248400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
17	chr20:16248000-16248600	Strong transcription	Fetal Muscle Trunk	muscle
18	chr20:16248000-16248800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr20:16248000-16248800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
20	chr20:16248000-16248800	ZNF genes & repeats	Lung	lung
21	chr20:16248000-16248800	ZNF genes & repeats	Spleen	Spleen
22	chr20:16248000-16249000	Strong transcription	Right Ventricle	heart
23	chr20:16248000-16254400	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links