Variant report

Variant	rs6539116
Chromosome Location	chr12:104391817-104391818
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr12:104391127-104391851	K562	blood:	n/a	n/a
2	ATF1	chr12:104391054-104391823	K562	blood:	n/a	n/a
3	MAX	chr12:104391597-104391871	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104391248..104393100-chr12:104457489..104459816,2	MCF-7	breast:

Variant related genes	Relation type
GLT8D2	TF binding region
ENSG00000111727	Chromatin interaction
ENSG00000120820	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10047614	1.00[ASN][1000 genomes]
rs1047490	1.00[CHB][hapmap];0.81[GIH][hapmap]
rs10861150	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10861151	1.00[ASN][1000 genomes]
rs11111867	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11111882	1.00[CHB][hapmap]
rs1165687	1.00[CHB][hapmap]
rs12312593	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs12366629	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369231	1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12372540	1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17805003	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]
rs1866074	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2629806	1.00[CHB][hapmap]
rs4135044	1.00[ASN][1000 genomes]
rs4135063	1.00[CHB][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs4135081	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[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	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132831	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs7136550	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7138850	1.00[ASN][1000 genomes]
rs7306515	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[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];1.00[CHB][hapmap]
rs7971994	0.83[CEU][hapmap];1.00[CHB][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
rs6539116	FAM71C	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104362000-104392800	Weak transcription	Fetal Brain Male	brain
2	chr12:104377800-104400200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:104380800-104395600	Weak transcription	Aorta	Aorta
4	chr12:104380800-104400200	Weak transcription	NHLF	lung
5	chr12:104381000-104400200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:104381600-104392800	Weak transcription	Left Ventricle	heart
7	chr12:104385000-104400200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:104385400-104400200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:104385600-104404000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:104385800-104400200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:104387000-104400200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:104387200-104404600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:104388800-104400200	Weak transcription	HSMM	muscle
14	chr12:104390400-104393000	Enhancers	Fetal Muscle Trunk	muscle
15	chr12:104390800-104392000	Enhancers	Fetal Lung	lung
16	chr12:104391200-104393000	Weak transcription	HSMMtube	muscle
17	chr12:104391200-104406200	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:104391400-104393200	Enhancers	Fetal Stomach	stomach
19	chr12:104391400-104393400	Enhancers	Fetal Muscle Leg	muscle
20	chr12:104391600-104392000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:104391600-104392600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:104391600-104406400	Weak transcription	Ovary	ovary
23	chr12:104391800-104392000	Enhancers	Fetal Heart	heart
24	chr12:104391800-104392000	Enhancers	K562	blood

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