Variant report

Variant	rs2613903
Chromosome Location	chr12:74945356-74945357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:74943223..74946956-chr12:74947283..74950877,6	K562	blood:
2	chr12:74936725..74942637-chr12:74943509..74950364,10	MCF-7	breast:
3	chr12:74938864..74942058-chr12:74943211..74947418,4	K562	blood:
4	chr12:74930467..74932875-chr12:74943697..74946304,2	MCF-7	breast:
5	chr12:74937896..74940364-chr12:74944289..74945994,2	K562	blood:
6	chr12:74943223..74946956-chr12:74948015..74950877,4	K562	blood:
7	chr12:74939663..74942006-chr12:74944132..74946349,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253719	Chromatin interaction
ENSG00000257386	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12816388	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1493797	0.90[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs1493805	0.81[ASN][1000 genomes]
rs1493806	0.93[ASW][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2605338	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605374	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2605376	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2605377	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2613882	0.90[CHB][hapmap]
rs2613887	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2613895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2613900	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2613901	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2641467	0.93[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2641468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2641481	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4882641	0.81[ASN][1000 genomes]
rs4882642	0.81[ASN][1000 genomes]
rs597888	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs628576	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs647129	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8744	0.92[CEU][hapmap];0.93[CHD][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039468	chr12:74080586-75000246	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv899293	chr12:74835107-74995760	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv899295	chr12:74854750-74984992	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv470303	chr12:74880668-74945356	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	n/a
5	nsv899296	chr12:74880668-74974630	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2613903	KLHDC10	trans	cerebellum	SCAN
rs2613903	ATXN7L3B	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:74936000-74945600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr12:74944800-74946200	Enhancers	Stomach Mucosa	stomach
3	chr12:74945000-74945400	Enhancers	Left Ventricle	heart

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