Variant report

Variant	rs2187091
Chromosome Location	chr18:44520048-44520049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10070	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs10164108	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10502879	0.85[CEU][hapmap]
rs10853545	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs10853547	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11082562	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11659693	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11660085	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12386118	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1465722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1539878	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1539881	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1970668	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2010834	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs2032215	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs2156049	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2156050	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2164104	1.00[CEU][hapmap]
rs2187092	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2571000	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2571024	0.81[ASN][1000 genomes]
rs2571028	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2576040	0.96[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes]
rs2576042	0.96[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes]
rs2576050	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2576051	0.81[ASN][1000 genomes]
rs477826	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs478820	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4890341	0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap]
rs4890343	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4890347	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4890698	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[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];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4890699	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4890700	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4890704	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4890706	0.84[EUR][1000 genomes]
rs4890707	0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs501062	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs501882	0.96[CEU][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs504668	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.97[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];0.94[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs513775	0.96[CEU][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs530205	0.96[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs541634	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs553456	0.81[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs578146	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs578451	0.96[CEU][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs58993513	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs590923	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs593340	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs605487	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs607780	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs616900	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs620228	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs626217	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap]
rs641366	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[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];0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs642897	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs644731	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs646128	0.96[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs649076	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs6507709	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs658756	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs680018	0.96[CEU][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs693503	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs695001	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs7227700	0.95[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs7240239	0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs7244013	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7244778	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7245049	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8086286	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8094654	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8095373	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8096263	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs892586	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9304336	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9304338	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9304339	0.84[ASN][1000 genomes]
rs9304340	0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9916891	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9945443	0.80[ASN][1000 genomes]
rs9947131	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9948103	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9948405	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9954336	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9959877	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9960463	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9966646	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs998819	0.95[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv833639	chr18:44426363-44552719	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv576813	chr18:44481641-44531283	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1057629	chr18:44500259-44539223	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1062444	chr18:44503472-44539223	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1062682	chr18:44509052-44539223	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1056744	chr18:44509052-44581752	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv909609	chr18:44513071-44597092	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	esv1818108	chr18:44519357-44549177	Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2187091	KATNAL2	cis	lymphoblastoid	seeQTL
rs2187091	ST8SIA5	cis	cerebellum	SCAN
rs2187091	ST8SIA5	cis	lymphoblastoid	seeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44515600-44520800	Weak transcription	Psoas Muscle	Psoas
2	chr18:44518400-44521000	Enhancers	HSMM	muscle
3	chr18:44518800-44520200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr18:44518800-44520400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr18:44518800-44520400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr18:44518800-44520800	Enhancers	NHLF	lung
7	chr18:44519000-44520200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr18:44519000-44520200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr18:44519000-44520200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr18:44519000-44520400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr18:44519000-44520800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr18:44519000-44520800	Enhancers	NHDF-Ad	bronchial
13	chr18:44519000-44521000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr18:44519000-44521000	Enhancers	Fetal Muscle Leg	muscle
15	chr18:44519000-44521200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr18:44519200-44520800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr18:44519200-44520800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr18:44519200-44520800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr18:44519400-44520200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr18:44519400-44520200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr18:44519400-44520200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr18:44519400-44520200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr18:44519400-44520200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr18:44519400-44520200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr18:44519400-44520200	Enhancers	Hela-S3	cervix
26	chr18:44519400-44520400	Enhancers	Osteobl	bone
27	chr18:44519400-44520800	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr18:44519600-44520200	Enhancers	H9 Cell Line	embryonic stem cell
29	chr18:44519600-44520400	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr18:44519600-44521000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr18:44519800-44520400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr18:44519800-44525400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr18:44520000-44520400	Flanking Active TSS	HSMMtube	muscle
34	chr18:44520000-44526200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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