Variant report

Variant	rs12621546
Chromosome Location	chr2:31265082-31265083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:31258340..31261335-chr2:31263112..31266010,2	K562	blood:

Variant related genes	Relation type
ENSG00000216093	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10197865	0.80[MEX][hapmap]
rs10198054	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10205584	0.80[ASN][1000 genomes]
rs10209881	0.92[MEX][hapmap]
rs10865086	0.84[YRI][hapmap]
rs11694302	0.80[ASN][1000 genomes]
rs11886970	0.80[ASN][1000 genomes]
rs11891469	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11898944	0.80[ASN][1000 genomes]
rs12464083	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12613732	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12617279	0.86[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12619377	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12621518	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12621813	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12712300	0.92[MEX][hapmap]
rs12712301	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712302	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12712303	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12712304	0.91[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12712305	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12712306	0.83[ASN][1000 genomes]
rs12999804	0.87[CEU][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs13009298	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13009779	0.82[CEU][hapmap]
rs1862966	0.81[ASW][hapmap];0.91[MEX][hapmap];0.80[YRI][hapmap]
rs1862967	0.81[ASW][hapmap];0.95[MEX][hapmap];0.80[YRI][hapmap]
rs1862968	0.81[ASW][hapmap];0.80[YRI][hapmap]
rs1862983	0.83[ASN][1000 genomes]
rs2194455	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4245766	0.82[CEU][hapmap];0.83[CHD][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs4268964	0.81[ASN][1000 genomes]
rs4951960	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4951961	0.80[ASN][1000 genomes]
rs4952031	0.83[MEX][hapmap]
rs4952040	0.83[ASN][1000 genomes]
rs5009910	0.81[ASW][hapmap];0.87[MEX][hapmap];0.80[YRI][hapmap]
rs62140633	0.80[ASN][1000 genomes]
rs6726690	0.80[ASN][1000 genomes]
rs6730186	0.80[ASN][1000 genomes]
rs6734015	0.83[ASN][1000 genomes]
rs6752303	0.87[MEX][hapmap]
rs72793304	0.80[ASN][1000 genomes]
rs7605643	0.92[MEX][hapmap]
rs7605982	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7608731	0.87[MEX][hapmap]
rs9679162	0.80[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12621546	GALNT14	cis	parietal	SCAN
rs12621546	PLLP	trans	cerebellum	SCAN
rs12621546	CAPN13	cis	parietal	SCAN
rs12621546	FAM179A	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31251400-31270000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:31260200-31265600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:31262000-31272200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr2:31264400-31265200	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr2:31264400-31266000	Enhancers	H9 Cell Line	embryonic stem cell
6	chr2:31264600-31265400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:31264600-31265800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr2:31264600-31265800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr2:31264800-31265400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:31264800-31265600	Enhancers	HUES48 Cell Line	embryonic stem cell

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