Variant report

Variant	rs6889029
Chromosome Location	chr5:95251238-95251239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95249666..95252549-chr5:95296490..95298581,2	K562	blood:
2	chr5:95248637..95251285-chr5:95252378..95254672,2	K562	blood:
3	chr5:95249774..95251634-chr5:95252118..95254823,2	MCF-7	breast:
4	chr5:95251039..95253504-chr5:95783165..95785479,2	K562	blood:

Variant related genes	Relation type
ENSG00000251314	Chromatin interaction
ENSG00000118985	Chromatin interaction

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];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10052503	0.91[CHB][hapmap]
rs10069748	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10070197	0.95[CEU][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10073752	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1043381	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10515232	0.91[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs1057963	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1057964	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11135441	0.90[CEU][hapmap];0.97[TSI][hapmap]
rs11135442	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11738768	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11738945	0.89[CEU][hapmap]
rs11739652	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11741563	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11741590	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.97[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];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13361341	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13361837	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1423268	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1423269	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]
rs1458017	0.91[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1458018	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]
rs1458019	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs147295	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs17085231	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]
rs17085249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17085266	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17085333	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs1841010	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2015159	0.94[EUR][1000 genomes]
rs2042340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2161318	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs2270554	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]
rs2348984	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2546191	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2546199	0.91[CHB][hapmap];0.82[CHD][hapmap]
rs2547997	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2548594	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]
rs2829	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777162	0.91[CHB][hapmap]
rs3777163	0.91[CHB][hapmap]
rs3777165	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs3777166	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs3777171	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs3777173	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs3777175	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap]
rs3777178	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs3777179	0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs3777182	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777183	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777192	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777193	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3777194	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]
rs3777196	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777197	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777201	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777202	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777203	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777204	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777207	0.80[CEU][hapmap]
rs3777208	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3815768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4538631	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs4563648	0.94[EUR][1000 genomes]
rs4642392	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]
rs56156268	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56219066	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6556893	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6861531	0.84[CEU][hapmap];0.91[CHB][hapmap]
rs6877329	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6879652	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6881872	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs6885567	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6890954	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7700895	0.84[CEU][hapmap];0.91[CHB][hapmap]
rs7702674	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7705279	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs7716691	1.00[CEU][hapmap];0.95[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];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs967546	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9986236	0.97[EUR][1000 genomes];0.86[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
rs6889029	ELL2	cis	lymphoblastoid	seeQTL
rs6889029	ELL2	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95214400-95251800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:95221600-95252200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr5:95222000-95252200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:95223000-95259800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr5:95226400-95263600	Weak transcription	Colonic Mucosa	Colon
6	chr5:95227400-95251600	Weak transcription	Primary T cells from cord blood	blood
7	chr5:95227400-95253800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr5:95231200-95254000	Weak transcription	Fetal Stomach	stomach
9	chr5:95232400-95255200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:95234200-95251800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr5:95234400-95251800	Weak transcription	Fetal Thymus	thymus
12	chr5:95235000-95251800	Weak transcription	Primary B cells from cord blood	blood
13	chr5:95236000-95251600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:95236200-95254200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:95236400-95276600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:95236800-95260000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr5:95237800-95251800	Weak transcription	K562	blood
18	chr5:95238200-95260400	Weak transcription	A549	lung
19	chr5:95238200-95282000	Weak transcription	HUVEC	blood vessel
20	chr5:95239400-95252000	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr5:95239600-95253200	Strong transcription	Osteobl	bone
22	chr5:95241000-95252000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:95242600-95251800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:95242600-95251800	Weak transcription	Spleen	Spleen
25	chr5:95242600-95259000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr5:95242600-95259800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:95243000-95255600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:95243000-95256800	Enhancers	Brain Substantia Nigra	brain
29	chr5:95243400-95278800	Weak transcription	Lung	lung
30	chr5:95243600-95274200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr5:95244400-95258600	Weak transcription	Fetal Intestine Large	intestine
32	chr5:95244800-95251400	Weak transcription	Stomach Mucosa	stomach
33	chr5:95244800-95260600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr5:95245000-95254600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:95245000-95256400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:95245200-95252200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr5:95245200-95259000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:95245400-95251800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:95245600-95251400	Weak transcription	Psoas Muscle	Psoas
40	chr5:95245600-95252600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:95245800-95251800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr5:95245800-95252400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:95245800-95255800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:95245800-95256200	Strong transcription	NHEK	skin
45	chr5:95246000-95252400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr5:95246400-95251800	Weak transcription	Ovary	ovary
47	chr5:95246400-95266400	Weak transcription	NHDF-Ad	bronchial
48	chr5:95246600-95251800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr5:95247200-95252200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr5:95247600-95251400	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links