Variant report

Variant	rs17129378
Chromosome Location	chr12:41861386-41861387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1026463	0.82[TSI][hapmap]
rs10506195	0.94[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs11615166	1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12811069	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12822018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12823312	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1379779	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1458170	0.94[CEU][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1598893	0.80[GIH][hapmap];0.82[TSI][hapmap]
rs17129392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17129427	0.94[CEU][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs17578886	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17768388	0.89[CEU][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1902905	1.00[CEU][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2468313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2710263	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs34057539	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34298736	0.85[EUR][1000 genomes]
rs34607783	0.85[EUR][1000 genomes]
rs34931927	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35002976	0.85[EUR][1000 genomes]
rs35667109	0.83[EUR][1000 genomes]
rs36038624	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57639356	0.85[EUR][1000 genomes]
rs58667777	0.85[EUR][1000 genomes]
rs67541586	0.84[EUR][1000 genomes]
rs71451530	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130614	0.96[ASN][1000 genomes]
rs7957589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs981013	0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3501985	chr12:41847710-41863530	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
3	esv3501996	chr12:41847724-41863526	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
4	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17129378	ABCD2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41858400-41863000	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr12:41859000-41862000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr12:41859400-41861400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:41859400-41862200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr12:41859800-41862000	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr12:41859800-41862000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:41859800-41862200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr12:41860000-41861400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr12:41860000-41861400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:41860000-41862200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:41860200-41861800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:41860200-41869200	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:41860400-41861400	Weak transcription	Brain Germinal Matrix	brain
14	chr12:41860400-41861600	Weak transcription	Fetal Lung	lung
15	chr12:41860800-41861600	Enhancers	H9 Cell Line	embryonic stem cell
16	chr12:41861000-41861400	Enhancers	Brain Anterior Caudate	brain
17	chr12:41861000-41861400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr12:41861000-41866600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:41861000-41866600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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