Variant report

Variant	rs2270554
Chromosome Location	chr5:95246134-95246135
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	chr5:95238043..95241007-chr5:95244981..95247839,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10035477	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10052503	0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap]
rs10069748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10070197	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10073752	0.83[CHB][hapmap]
rs1043381	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10515232	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs1057963	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1057964	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11135441	0.90[CEU][hapmap];1.00[TSI][hapmap]
rs11135442	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11738768	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11738945	0.89[CEU][hapmap]
rs11739652	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11741563	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11741590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11742959	0.89[CEU][hapmap]
rs11744881	0.83[ASW][hapmap];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]
rs13361341	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361837	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1423269	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]
rs1458017	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458019	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs147295	1.00[ASW][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.82[EUR][1000 genomes]
rs17085231	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs17085249	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17085266	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17085333	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs1841010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015159	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2042340	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2161318	0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap]
rs2348984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2546191	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2546199	0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap]
rs2547997	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2548594	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2829	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777162	0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap]
rs3777163	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs3777165	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs3777166	0.83[CHB][hapmap]
rs3777171	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs3777173	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs3777175	0.83[CHB][hapmap]
rs3777178	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs3777179	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap]
rs3777182	0.94[EUR][1000 genomes]
rs3777183	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[EUR][1000 genomes]
rs3777184	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777185	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777188	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]
rs3777189	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777190	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]
rs3777192	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3777193	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777194	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777196	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777197	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777200	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]
rs3777201	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3777202	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777203	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777207	0.80[CEU][hapmap]
rs3777208	0.92[EUR][1000 genomes]
rs3815768	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4563648	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4642392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56156268	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56219066	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6556893	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6861531	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs6877329	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6879652	1.00[CEU][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6881872	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs6885567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6889029	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6890954	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7700895	0.84[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7702674	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7705279	0.87[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap]
rs7716691	1.00[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7724599	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs889302	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9314162	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs967546	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9986236	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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
rs2270554	ELL2	cis	Liver	GTEx
rs2270554	ERAP1	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95214400-95247800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:95214400-95251800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:95218200-95246200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:95221600-95252200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr5:95222000-95252200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:95223000-95259800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:95226400-95263600	Weak transcription	Colonic Mucosa	Colon
8	chr5:95227400-95251600	Weak transcription	Primary T cells from cord blood	blood
9	chr5:95227400-95253800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:95231200-95254000	Weak transcription	Fetal Stomach	stomach
11	chr5:95232400-95255200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr5:95232600-95247400	Weak transcription	Aorta	Aorta
13	chr5:95234200-95251800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr5:95234400-95251800	Weak transcription	Fetal Thymus	thymus
15	chr5:95235000-95251800	Weak transcription	Primary B cells from cord blood	blood
16	chr5:95236000-95247600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr5:95236000-95251600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:95236200-95254200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:95236400-95249600	Weak transcription	Fetal Lung	lung
20	chr5:95236400-95276600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:95236800-95260000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:95237800-95251800	Weak transcription	K562	blood
23	chr5:95238200-95260400	Weak transcription	A549	lung
24	chr5:95238200-95282000	Weak transcription	HUVEC	blood vessel
25	chr5:95239400-95246200	Weak transcription	Fetal Intestine Small	intestine
26	chr5:95239400-95252000	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr5:95239600-95249600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:95239600-95253200	Strong transcription	Osteobl	bone
29	chr5:95239800-95247600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr5:95240000-95250600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr5:95240600-95246400	Strong transcription	NHDF-Ad	bronchial
32	chr5:95241000-95246200	Weak transcription	Left Ventricle	heart
33	chr5:95241000-95252000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:95241200-95248200	Genic enhancers	Muscle Satellite Cultured Cells	--
35	chr5:95241600-95246800	Enhancers	Brain Hippocampus Middle	brain
36	chr5:95241600-95249200	Genic enhancers	Liver	Liver
37	chr5:95242400-95248000	Strong transcription	NHLF	lung
38	chr5:95242400-95248600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:95242600-95248600	Strong transcription	Placenta	Placenta
40	chr5:95242600-95251000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr5:95242600-95251800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:95242600-95251800	Weak transcription	Spleen	Spleen
43	chr5:95242600-95259000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:95242600-95259800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr5:95242800-95246800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:95242800-95249000	Enhancers	Brain Cingulate Gyrus	brain
47	chr5:95243000-95255600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:95243000-95256800	Enhancers	Brain Substantia Nigra	brain
49	chr5:95243200-95246400	Enhancers	Brain Anterior Caudate	brain
50	chr5:95243200-95246400	Genic enhancers	HSMM	muscle

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