Variant report

Variant	rs2932126
Chromosome Location	chr18:44703784-44703785
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:44675372..44679287-chr18:44700113..44704114,10	MCF-7	breast:
2	chr18:44675848..44678361-chr18:44699497..44704011,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167220	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11663321	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12960378	0.96[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs12960444	0.84[ASN][1000 genomes]
rs12963648	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12964465	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16954921	0.81[GIH][hapmap]
rs16954999	0.81[GIH][hapmap]
rs17785419	0.85[CEU][hapmap]
rs2251948	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2277717	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2461247	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2571001	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2571009	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2571016	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2576030	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2576031	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2576053	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576056	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2576060	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2635040	1.00[JPT][hapmap]
rs2635041	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2635042	1.00[JPT][hapmap]
rs2635043	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2635045	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2635046	0.85[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2635047	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2635049	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2635050	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2668761	0.81[GIH][hapmap]
rs2668779	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2684818	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2684820	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2684822	0.96[ASN][1000 genomes]
rs2684825	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2684826	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2684837	0.87[CEU][hapmap]
rs28702976	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3816125	0.96[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap]
rs7242978	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7504798	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs9304341	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9960264	0.96[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv3412252	chr18:44684003-44711534	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2932126	KATNAL2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44702800-44706200	Weak transcription	Lung	lung
2	chr18:44703000-44705600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr18:44703000-44705600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr18:44703000-44705600	Weak transcription	Fetal Stomach	stomach
5	chr18:44703000-44706000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr18:44703200-44705600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr18:44703600-44703800	Active TSS	Primary T cells from cord blood	blood

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