Variant report

Variant	rs12471388
Chromosome Location	chr2:62754382-62754383
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	chr2:62704342..62706452-chr2:62754293..62757210,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11904315	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12151765	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12613959	0.85[ASN][1000 genomes]
rs13429359	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17025780	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs17025805	0.81[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4494727	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55776722	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58257459	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62178042	0.88[ASN][1000 genomes]
rs6708322	0.97[ASN][1000 genomes]
rs6708968	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6726083	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6750204	0.81[JPT][hapmap]
rs6752833	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6753189	0.94[ASN][1000 genomes]
rs72885263	0.93[ASN][1000 genomes]
rs72885271	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs901532	0.90[CHD][hapmap];0.85[JPT][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	esv2760551	chr2:62741167-62760232	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv834226	chr2:62745027-62894013	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv3336776	chr2:62747914-62813461	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv527200	chr2:62751619-62758044	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12471388	TMEM17	cis	parietal	SCAN
rs12471388	CEP68	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62749200-62760400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:62752200-62754800	Weak transcription	HUVEC	blood vessel
3	chr2:62752600-62755400	Enhancers	Stomach Mucosa	stomach
4	chr2:62752800-62754600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr2:62752800-62754800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:62752800-62755400	Enhancers	A549	lung
7	chr2:62752800-62755600	Enhancers	Fetal Lung	lung
8	chr2:62753000-62755400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:62753200-62755000	Enhancers	K562	blood
10	chr2:62753600-62754800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:62753600-62755200	Weak transcription	Fetal Intestine Large	intestine
12	chr2:62753600-62756000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:62753600-62756200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:62753600-62757600	Enhancers	HepG2	liver
15	chr2:62753800-62754400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:62753800-62755400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:62754000-62755000	Weak transcription	Fetal Intestine Small	intestine
18	chr2:62754000-62755800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:62754000-62756000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:62754000-62756200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:62754000-62756400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:62754000-62756400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:62754000-62756800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:62754200-62755200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:62754200-62756200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:62754200-62756200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:62754200-62758400	Weak transcription	Pancreas	Pancrea
28	chr2:62754200-62766800	Weak transcription	Ovary	ovary

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