Variant report

Variant	rs1423269
Chromosome Location	chr5:95255724-95255725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10035477	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10052503	0.91[CHB][hapmap]
rs10069748	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10070197	0.95[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10073752	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs1043381	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10515232	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs1057963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1057964	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11135441	0.90[CEU][hapmap];1.00[TSI][hapmap]
rs11135442	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11738768	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11738945	0.89[CEU][hapmap]
rs11739652	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11741563	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11741590	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11742959	0.89[CEU][hapmap]
rs11744881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13361341	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13361837	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1423268	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1458017	0.91[CHB][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1458018	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1458019	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs147295	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs17085231	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17085249	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17085266	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17085333	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.80[YRI][hapmap]
rs1841010	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2015159	0.94[EUR][1000 genomes]
rs2042340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2161318	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs2270554	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2348984	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2546191	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2546199	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs2547997	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2548594	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2829	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777162	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs3777163	0.91[CHB][hapmap]
rs3777165	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.80[YRI][hapmap]
rs3777166	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3777171	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.80[YRI][hapmap]
rs3777173	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap]
rs3777175	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap]
rs3777178	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs3777179	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs3777182	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777183	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777190	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777192	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777193	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777194	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777196	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777197	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777201	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777202	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777203	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777204	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777207	0.80[CEU][hapmap]
rs3777208	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3815768	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4538631	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs4563648	0.94[EUR][1000 genomes]
rs4642392	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56156268	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56219066	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6556893	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6861531	0.84[CEU][hapmap];0.91[CHB][hapmap]
rs6877329	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6879652	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6881872	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.80[YRI][hapmap]
rs6885567	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6889029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6890954	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7700895	0.84[CEU][hapmap];0.91[CHB][hapmap]
rs7702674	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7705279	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs7716691	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7724599	0.91[CHB][hapmap]
rs889302	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[EUR][1000 genomes]
rs9314162	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs967546	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9986236	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1423269	ELL2	cis	multi-tissue	Pritchard
rs1423269	ELL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95223000-95259800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr5:95226400-95263600	Weak transcription	Colonic Mucosa	Colon
3	chr5:95236400-95276600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:95236800-95260000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr5:95238200-95260400	Weak transcription	A549	lung
6	chr5:95238200-95282000	Weak transcription	HUVEC	blood vessel
7	chr5:95242600-95259000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:95242600-95259800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:95243000-95256800	Enhancers	Brain Substantia Nigra	brain
10	chr5:95243400-95278800	Weak transcription	Lung	lung
11	chr5:95243600-95274200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr5:95244400-95258600	Weak transcription	Fetal Intestine Large	intestine
13	chr5:95244800-95260600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr5:95245000-95256400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:95245200-95259000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:95245800-95255800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:95245800-95256200	Strong transcription	NHEK	skin
18	chr5:95246400-95266400	Weak transcription	NHDF-Ad	bronchial
19	chr5:95249800-95271600	Weak transcription	NH-A	brain
20	chr5:95250600-95263000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr5:95251200-95259000	Weak transcription	Fetal Intestine Small	intestine
22	chr5:95251200-95260200	Genic enhancers	Liver	Liver
23	chr5:95251200-95261800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:95251400-95260200	Genic enhancers	HepG2	liver
25	chr5:95251600-95259000	Weak transcription	Stomach Mucosa	stomach
26	chr5:95251800-95257200	Strong transcription	Hela-S3	cervix
27	chr5:95251800-95259000	Weak transcription	Right Ventricle	heart
28	chr5:95252000-95258600	Weak transcription	NHLF	lung
29	chr5:95252200-95256200	Weak transcription	Esophagus	oesophagus
30	chr5:95252200-95256600	Weak transcription	Spleen	Spleen
31	chr5:95252200-95263800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:95252200-95272400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr5:95252400-95256200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:95252400-95256200	Weak transcription	Aorta	Aorta
35	chr5:95252400-95256200	Weak transcription	Gastric	stomach
36	chr5:95252400-95256200	Weak transcription	Left Ventricle	heart
37	chr5:95252400-95256200	Weak transcription	Pancreas	Pancrea
38	chr5:95252400-95256200	Strong transcription	HMEC	breast
39	chr5:95252400-95256600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:95252400-95257200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:95252400-95259000	Weak transcription	Psoas Muscle	Psoas
42	chr5:95252400-95259600	Weak transcription	Fetal Thymus	thymus
43	chr5:95252400-95260400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr5:95252400-95260600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:95252400-95264600	Weak transcription	Ovary	ovary
46	chr5:95252400-95266400	Weak transcription	HSMMtube	muscle
47	chr5:95252600-95256200	Weak transcription	Right Atrium	heart
48	chr5:95252600-95259400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr5:95253000-95258600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:95253200-95259200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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