Variant report

Variant	rs28370654
Chromosome Location	chr12:40403828-40403829
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	12:40402537-40410050..12:40703633-40711447	GM12878	blood:
2	12:40402537-40410050..12:40497414-40501128	K562	blood:
3	12:40402537-40410050..12:40687302-40691796	GM12878	blood:
4	chr12:40401380..40404194-chr12:40458458..40460119,2	K562	blood:
5	12:40402537-40410050..12:40793507-40812339	GM12878	blood:

Variant related genes	Relation type
ENSG00000151229	Chromatin interaction
ENSG00000188906	Chromatin interaction
ENSG00000205592	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10506145	0.93[CEU][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10877837	0.82[ASN][1000 genomes]
rs11174370	1.00[JPT][hapmap]
rs11564133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11564137	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11564139	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11564160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11564194	1.00[JPT][hapmap]
rs11564223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12312535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810368	1.00[JPT][hapmap]
rs12827948	1.00[JPT][hapmap]
rs1482282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1491926	0.93[AFR][1000 genomes]
rs17442108	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17442304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs17442469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442805	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17443112	0.93[AFR][1000 genomes]
rs17458299	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs17458396	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17458403	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17461082	1.00[CHB][hapmap]
rs17461492	0.93[AFR][1000 genomes]
rs17465400	0.93[AFR][1000 genomes]
rs17465519	0.85[AFR][1000 genomes]
rs17465540	0.85[AFR][1000 genomes]
rs17483628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046929	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2086598	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2404346	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404574	0.93[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2708404	1.00[JPT][hapmap]
rs28370607	0.82[ASN][1000 genomes]
rs28370611	0.82[ASN][1000 genomes]
rs28370644	1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28370659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28740188	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55707305	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55993200	0.93[AFR][1000 genomes]
rs7305377	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7969495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974522	0.93[AFR][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	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1052202	chr12:40322607-40406760	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv899027	chr12:40388510-40428561	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40384400-40405200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:40384400-40405400	Weak transcription	Pancreas	Pancrea
3	chr12:40393400-40405400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:40394000-40405400	Weak transcription	Left Ventricle	heart
5	chr12:40394000-40410800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:40394400-40405000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:40394400-40405200	Weak transcription	Hela-S3	cervix
8	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:40395200-40405400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:40402200-40425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:40403800-40404200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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