Variant report

Variant	rs17129427
Chromosome Location	chr12:41908624-41908625
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	chr12:41903994..41905628-chr12:41905672..41908634,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1026463	0.84[CEU][hapmap];0.89[MEX][hapmap]
rs10506195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11615166	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12811069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12822018	0.86[ASW][hapmap];0.94[CEU][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12823312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1379779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1458170	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1598893	0.89[MEX][hapmap]
rs17129378	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]
rs17129392	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17129456	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs17578886	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs17768388	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1902905	0.86[ASW][hapmap];0.94[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2468313	1.00[JPT][hapmap]
rs2710263	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs34057539	0.90[EUR][1000 genomes]
rs34298736	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34607783	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34931927	0.87[EUR][1000 genomes]
rs35002976	0.98[EUR][1000 genomes]
rs35032376	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35667109	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35753665	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36020206	0.83[EUR][1000 genomes]
rs36038624	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57639356	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58667777	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67541586	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7957589	0.94[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs981013	0.84[CEU][hapmap];0.89[MEX][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	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
3	nsv826349	chr12:41878846-41911495	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	nsv899040	chr12:41905897-42181706	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	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
rs17129427	ABCD2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41898600-41915400	Weak transcription	Aorta	Aorta
2	chr12:41902000-41909400	Enhancers	Brain Germinal Matrix	brain
3	chr12:41902400-41915000	Weak transcription	Brain Anterior Caudate	brain
4	chr12:41904400-41908800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr12:41904600-41915600	Weak transcription	Fetal Kidney	kidney
6	chr12:41905200-41916400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:41906800-41909000	Enhancers	Fetal Brain Female	brain
8	chr12:41907200-41909000	Enhancers	Fetal Brain Male	brain
9	chr12:41907800-41908800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr12:41907800-41915400	Weak transcription	Fetal Stomach	stomach
11	chr12:41908000-41908800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr12:41908000-41915400	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:41908000-41915800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:41908200-41915400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr12:41908400-41909600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:41908400-41909600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:41908600-41909400	Weak transcription	Brain Substantia Nigra	brain
18	chr12:41908600-41909800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:41908600-41910000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:41908600-41915400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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