Variant report

Variant	rs17805003
Chromosome Location	chr12:104393887-104393888
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104388319..104390087-chr12:104391982..104393996,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10047614	1.00[ASN][1000 genomes]
rs10861150	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs10861151	1.00[ASN][1000 genomes]
rs11111867	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12312593	0.83[CEU][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs12366629	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369231	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12372540	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866074	1.00[ASN][1000 genomes]
rs4135044	1.00[ASN][1000 genomes]
rs4135063	0.84[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs4135081	0.84[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs4135093	1.00[ASN][1000 genomes]
rs55684344	1.00[ASN][1000 genomes]
rs56219801	1.00[ASN][1000 genomes]
rs56369424	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539116	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132831	0.83[CEU][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs7136550	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs7138850	1.00[ASN][1000 genomes]
rs7306515	0.84[CEU][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs7313381	1.00[ASN][1000 genomes]
rs7953572	0.83[CEU][hapmap]
rs7971994	0.83[CEU][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17805003	FAM71C	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104377800-104400200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:104380800-104395600	Weak transcription	Aorta	Aorta
3	chr12:104380800-104400200	Weak transcription	NHLF	lung
4	chr12:104381000-104400200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:104385000-104400200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:104385400-104400200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:104385600-104404000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:104385800-104400200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:104387000-104400200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:104387200-104404600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:104388800-104400200	Weak transcription	HSMM	muscle
12	chr12:104391200-104406200	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:104391600-104406400	Weak transcription	Ovary	ovary
14	chr12:104392600-104395200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:104393000-104407400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:104393200-104400200	Weak transcription	Fetal Stomach	stomach
17	chr12:104393400-104400200	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links