Variant report

Variant	rs12109029
Chromosome Location	chr5:119786093-119786094
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	chr5:119785992..119787497-chr5:119792334..119794755,2	K562	blood:
2	chr5:119784118..119786225-chr5:119788090..119789969,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10036322	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10447269	0.90[EUR][1000 genomes]
rs10478464	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12523269	1.00[CHB][hapmap]
rs13357775	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13359009	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13435941	0.82[EUR][1000 genomes]
rs1347070	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs1368189	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1394115	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1404300	1.00[CHB][hapmap]
rs1432457	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1432461	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1432464	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17146635	0.89[ASN][1000 genomes]
rs17146644	0.89[ASN][1000 genomes]
rs17146710	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1902147	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2082353	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2082356	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2601208	1.00[JPT][hapmap]
rs2601210	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2601211	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2604163	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2655067	1.00[JPT][hapmap]
rs2655069	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35399227	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41357149	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4895250	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4895253	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4895261	1.00[JPT][hapmap]
rs59336675	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6595232	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6595236	1.00[CHB][hapmap]
rs6865215	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6883068	0.94[ASW][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.82[MKK][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs6895493	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7446731	0.83[EUR][1000 genomes]
rs753641	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7701804	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7710928	1.00[CHB][hapmap]
rs7727978	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7733602	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9327142	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs982827	0.82[AMR][1000 genomes];0.85[EUR][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	nsv532200	chr5:119317901-120102513	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1018955	chr5:119679918-119802014	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1018100	chr5:119749898-119802014	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12109029	FAM170A	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:119780400-119786400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr5:119780800-119786200	Enhancers	HSMM	muscle
3	chr5:119781000-119786200	Enhancers	HSMMtube	muscle
4	chr5:119782600-119786200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr5:119782800-119790000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:119783000-119793600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:119783800-119789200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:119783800-119790000	Weak transcription	NHLF	lung
9	chr5:119784000-119788000	Weak transcription	NH-A	brain
10	chr5:119784400-119787000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:119785000-119786200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:119785200-119786800	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr5:119785200-119787400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr5:119785400-119786600	Weak transcription	Psoas Muscle	Psoas
15	chr5:119785600-119789200	Weak transcription	NHDF-Ad	bronchial
16	chr5:119785600-119789400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:119785600-119789800	Weak transcription	Osteobl	bone
18	chr5:119785800-119788800	Weak transcription	Fetal Heart	heart
19	chr5:119785800-119789600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:119785800-119789800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:119786000-119786600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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