Variant report

Variant	rs17085231
Chromosome Location	chr5:95222156-95222157
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	chr5:95219720..95223922-chr5:95224301..95226439,3	MCF-7	breast:
2	chr5:95212190..95213733-chr5:95220441..95223038,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10035477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069748	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10070197	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs1043381	1.00[CEU][hapmap];0.90[CHB][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1057963	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1057964	1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11135441	0.90[CEU][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11135442	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738768	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11738945	0.89[CEU][hapmap]
rs11739652	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11741563	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11741590	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs11742959	0.89[CEU][hapmap]
rs11744881	0.89[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13361341	0.95[EUR][1000 genomes]
rs13361837	0.94[EUR][1000 genomes]
rs1423268	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1423269	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]
rs1458017	0.81[EUR][1000 genomes]
rs1458018	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1458019	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs147295	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs154460	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17085249	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17085266	0.95[EUR][1000 genomes]
rs17085333	0.88[MEX][hapmap]
rs1841010	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2015159	0.90[EUR][1000 genomes]
rs2042340	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2270554	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2348984	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2546191	0.99[EUR][1000 genomes]
rs2547997	0.95[EUR][1000 genomes]
rs2548594	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2829	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3777165	0.88[MEX][hapmap]
rs3777166	0.86[YRI][hapmap]
rs3777171	0.88[MEX][hapmap]
rs3777173	0.82[MEX][hapmap]
rs3777175	0.82[LWK][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap]
rs3777178	0.83[CEU][hapmap]
rs3777179	0.84[CEU][hapmap];0.88[MEX][hapmap]
rs3777182	0.90[EUR][1000 genomes]
rs3777183	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs3777184	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3777185	0.89[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3777188	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]
rs3777189	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3777190	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]
rs3777192	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3777193	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs3777194	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs3777196	1.00[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs3777197	0.99[EUR][1000 genomes]
rs3777200	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3777201	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3777202	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3777203	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3777204	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs3777207	0.80[CEU][hapmap]
rs3777208	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3815768	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4563648	0.90[EUR][1000 genomes]
rs4642392	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs56156268	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56219066	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6556893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861531	0.84[CEU][hapmap]
rs6877329	0.95[EUR][1000 genomes]
rs6879652	1.00[CEU][hapmap];0.90[CHB][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6881872	0.88[MEX][hapmap]
rs6885567	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6889029	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6890954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7700895	0.84[CEU][hapmap]
rs7702674	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7716691	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs889302	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs9314162	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs967546	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9986236	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17085231	ELL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95212000-95224000	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr5:95212400-95223800	Weak transcription	Brain Substantia Nigra	brain
3	chr5:95213000-95244600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:95214400-95224800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:95214400-95234200	Weak transcription	Fetal Brain Female	brain
6	chr5:95214400-95247800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:95214400-95251800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:95214600-95225000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr5:95214600-95230400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:95214800-95226000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:95215000-95230200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:95215200-95223600	Weak transcription	A549	lung
13	chr5:95215200-95234200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:95215600-95226000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:95215600-95226000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr5:95215800-95244600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:95216600-95225800	Weak transcription	Colonic Mucosa	Colon
18	chr5:95216800-95223600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:95217000-95223800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:95217800-95225600	Weak transcription	Lung	lung
21	chr5:95217800-95230000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:95218000-95222200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:95218000-95225400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr5:95218000-95225800	Weak transcription	Aorta	Aorta
25	chr5:95218000-95226200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr5:95218000-95231000	Weak transcription	Right Atrium	heart
27	chr5:95218000-95242200	Weak transcription	Spleen	Spleen
28	chr5:95218200-95224400	Weak transcription	Brain Anterior Caudate	brain
29	chr5:95218200-95224800	Weak transcription	Brain Hippocampus Middle	brain
30	chr5:95218200-95231600	Weak transcription	Fetal Heart	heart
31	chr5:95218200-95246200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:95219200-95225600	Weak transcription	Pancreas	Pancrea
33	chr5:95219200-95226000	Weak transcription	Brain Angular Gyrus	brain
34	chr5:95219200-95229600	Weak transcription	Esophagus	oesophagus
35	chr5:95219600-95223600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:95219600-95225800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr5:95219800-95223600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:95219800-95223800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:95219800-95244400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:95220000-95225400	Weak transcription	HUVEC	blood vessel
41	chr5:95220000-95227400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr5:95220000-95242000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:95220000-95245200	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr5:95220200-95223600	Weak transcription	Gastric	stomach
45	chr5:95220200-95223800	Weak transcription	Primary B cells from cord blood	blood
46	chr5:95220200-95224400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr5:95220200-95225600	Weak transcription	Primary T cells from cord blood	blood
48	chr5:95220200-95225600	Weak transcription	Right Ventricle	heart
49	chr5:95220200-95225800	Weak transcription	Ovary	ovary
50	chr5:95220200-95230600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links