Variant report

Variant	rs3816125
Chromosome Location	chr18:44601611-44601612
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	chr18:44599383..44602020-chr18:44603317..44605439,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11663321	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12960378	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]
rs12960444	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12963648	0.96[EUR][1000 genomes]
rs12964465	0.97[EUR][1000 genomes]
rs16954921	0.81[GIH][hapmap]
rs16954999	0.81[GIH][hapmap]
rs17785419	0.81[CEU][hapmap]
rs2251948	0.96[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2277717	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2289133	0.86[GIH][hapmap]
rs2461247	0.93[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2571001	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2571009	0.85[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs2571016	1.00[CEU][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs2576030	1.00[CEU][hapmap];0.83[JPT][hapmap];0.96[EUR][1000 genomes]
rs2576031	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2576053	0.82[EUR][1000 genomes]
rs2576056	0.96[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2576060	1.00[CEU][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs2635040	0.92[CHB][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2635041	0.84[EUR][1000 genomes]
rs2635042	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2635043	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2635045	0.86[EUR][1000 genomes]
rs2635046	0.82[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap]
rs2635047	0.83[EUR][1000 genomes]
rs2635049	0.96[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2635050	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2668761	0.81[GIH][hapmap]
rs2668779	0.83[EUR][1000 genomes]
rs2684818	0.96[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs2684820	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2684825	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2684826	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2684837	0.83[CEU][hapmap]
rs28693565	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28702976	0.96[EUR][1000 genomes]
rs2932126	0.96[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap]
rs4986203	0.85[TSI][hapmap]
rs7242978	1.00[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs7504798	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9304341	0.86[EUR][1000 genomes]
rs9960264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9962602	0.84[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	nsv909610	chr18:44549455-44602249	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3816125	KATNAL2	cis	parietal	SCAN
rs3816125	PIAS2	cis	multi-tissue	Pritchard

Chromatin state (count:41 , 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	chr18:44587800-44603400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr18:44588200-44621600	Weak transcription	Left Ventricle	heart
7	chr18:44591800-44602800	Weak transcription	Brain Angular Gyrus	brain
8	chr18:44594200-44603800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr18:44594400-44603200	Weak transcription	Brain Substantia Nigra	brain
10	chr18:44594600-44602800	Weak transcription	Adipose Nuclei	Adipose
11	chr18:44598200-44630000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr18:44599800-44602000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr18:44600000-44602600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr18:44600400-44601800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr18:44601000-44602800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr18:44601400-44601800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr18:44601400-44602200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr18:44601400-44602200	Enhancers	NHEK	skin
19	chr18:44601400-44602400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr18:44601400-44602400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr18:44601400-44602400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr18:44601400-44602400	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr18:44601400-44602400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr18:44601400-44602400	Enhancers	HSMMtube	muscle
25	chr18:44601400-44608000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr18:44601600-44601800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr18:44601600-44601800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr18:44601600-44602000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr18:44601600-44602200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr18:44601600-44602200	Enhancers	H9 Cell Line	embryonic stem cell
31	chr18:44601600-44602200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr18:44601600-44602200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr18:44601600-44602200	Enhancers	Fetal Muscle Trunk	muscle
34	chr18:44601600-44602200	Enhancers	Fetal Muscle Leg	muscle
35	chr18:44601600-44602400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr18:44601600-44602400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr18:44601600-44602400	Flanking Active TSS	Hela-S3	cervix
38	chr18:44601600-44602600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr18:44601600-44602800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr18:44601600-44603000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr18:44601600-44603200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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