Variant report

Variant	rs12487108
Chromosome Location	chr3:52063886-52063887
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52037550..52040223-chr3:52062466..52064386,2	K562	blood:
2	chr3:52049402..52051939-chr3:52063118..52065044,2	K562	blood:
3	chr3:52063062..52064690-chr3:52126116..52128570,2	K562	blood:
4	chr3:52060421..52065315-chr3:52077239..52080916,4	K562	blood:
5	chr3:52063546..52065859-chr3:52080631..52082453,2	MCF-7	breast:
6	chr3:52063502..52067953-chr3:52083827..52087506,5	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12492696	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2334959	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2334960	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687606	0.89[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687798	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687799	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66514320	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs66530305	0.80[AMR][1000 genomes]
rs6792935	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72622936	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs745618	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7642881	0.82[AMR][1000 genomes]
rs9848727	0.83[AMR][1000 genomes]
rs9866081	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
9	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52050600-52073400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:52056600-52064400	Weak transcription	Pancreas	Pancrea
3	chr3:52056600-52066400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:52060000-52065200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:52060600-52066000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:52061600-52068600	Enhancers	Fetal Muscle Leg	muscle
7	chr3:52062200-52064600	Enhancers	Brain Substantia Nigra	brain
8	chr3:52062200-52073800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr3:52062400-52064000	Enhancers	Brain Hippocampus Middle	brain
10	chr3:52062400-52064000	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:52062400-52064000	Enhancers	K562	blood
12	chr3:52062400-52064400	Enhancers	Spleen	Spleen
13	chr3:52062400-52064600	Enhancers	Right Atrium	heart
14	chr3:52062400-52064800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:52062400-52065400	Enhancers	Psoas Muscle	Psoas
16	chr3:52062400-52065600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:52062400-52065600	Enhancers	NHEK	skin
18	chr3:52062400-52066000	Enhancers	HMEC	breast
19	chr3:52062600-52065600	Enhancers	Esophagus	oesophagus
20	chr3:52062800-52064000	Enhancers	Right Ventricle	heart
21	chr3:52062800-52066800	Weak transcription	Fetal Brain Female	brain
22	chr3:52063000-52066600	Weak transcription	Fetal Brain Male	brain
23	chr3:52063000-52067800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr3:52063200-52064000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:52063200-52064400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:52063200-52065800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:52063200-52066400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:52063200-52066800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:52063400-52066400	Weak transcription	Fetal Heart	heart
30	chr3:52063600-52064000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:52063600-52065000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:52063600-52066000	Weak transcription	Brain Angular Gyrus	brain
33	chr3:52063600-52066000	Enhancers	Fetal Muscle Trunk	muscle
34	chr3:52063600-52066200	Weak transcription	Brain Anterior Caudate	brain
35	chr3:52063600-52066200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:52063600-52067600	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr3:52063600-52072400	Weak transcription	HSMM	muscle
38	chr3:52063800-52064800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:52063800-52064800	Weak transcription	Left Ventricle	heart
40	chr3:52063800-52065600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr3:52063800-52065600	Enhancers	HepG2	liver
42	chr3:52063800-52066600	Weak transcription	HSMMtube	muscle

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