Variant report

Variant	rs12960378
Chromosome Location	chr18:44614090-44614091
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	chr18:44612247..44614708-chr18:44617059..44619635,2	K562	blood:

Variant related genes	Relation type
ENSG00000266957	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11663321	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12960444	0.97[EUR][1000 genomes]
rs12963648	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12964465	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13381713	0.83[GIH][hapmap]
rs16954921	0.86[GIH][hapmap]
rs16954999	0.86[GIH][hapmap]
rs17785419	0.81[CEU][hapmap]
rs2251948	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277717	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289133	0.80[GIH][hapmap]
rs2461247	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2571001	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571009	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2571016	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2576030	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2576031	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576053	0.83[EUR][1000 genomes]
rs2576056	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576060	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2635040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635041	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2635042	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2635043	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635045	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2635046	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2635047	0.84[EUR][1000 genomes]
rs2635049	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635050	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668761	0.86[GIH][hapmap]
rs2668779	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2684818	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2684820	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684822	0.82[ASN][1000 genomes]
rs2684825	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684826	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684837	0.83[CEU][hapmap]
rs28693565	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28702976	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2932126	0.96[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs3816125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7242978	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7504798	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9304341	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9960264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9962602	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv909611	chr18:44560875-44614090	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv909612	chr18:44560875-44681485	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1067278	chr18:44564162-44629283	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv576819	chr18:44602249-44677627	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12960378	KATNAL2	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44579800-44630200	Weak transcription	Right Ventricle	heart
2	chr18:44586800-44629600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr18:44587200-44630600	Weak transcription	Brain Anterior Caudate	brain
4	chr18:44587600-44629400	Weak transcription	Liver	Liver
5	chr18:44588200-44621600	Weak transcription	Left Ventricle	heart
6	chr18:44598200-44630000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr18:44602200-44630000	Weak transcription	Fetal Muscle Leg	muscle
8	chr18:44603400-44614200	Weak transcription	Brain Substantia Nigra	brain
9	chr18:44603800-44614400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr18:44603800-44630000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr18:44604000-44630200	Weak transcription	Adipose Nuclei	Adipose
12	chr18:44604000-44630600	Weak transcription	Brain Angular Gyrus	brain
13	chr18:44604800-44630800	Weak transcription	Brain Hippocampus Middle	brain
14	chr18:44605400-44630400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr18:44607600-44637600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr18:44609200-44638400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr18:44611000-44630000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr18:44611000-44633000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr18:44611400-44633000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr18:44611600-44630600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr18:44611600-44635600	Weak transcription	Psoas Muscle	Psoas
22	chr18:44612600-44632600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr18:44613400-44614600	Weak transcription	Fetal Kidney	kidney
24	chr18:44613800-44638200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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