Variant report

Variant	rs2548279
Chromosome Location	chr5:100177519-100177520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10043056	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10044903	0.95[EUR][1000 genomes]
rs10052474	0.95[EUR][1000 genomes]
rs10057237	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs10058901	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10059470	0.80[EUR][1000 genomes]
rs10059846	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10069305	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10075853	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs10078251	0.84[EUR][1000 genomes]
rs10078934	0.93[CEU][hapmap];0.96[EUR][1000 genomes]
rs10214216	0.81[EUR][1000 genomes]
rs10463771	0.96[EUR][1000 genomes]
rs10463772	0.96[EUR][1000 genomes]
rs10478598	0.85[EUR][1000 genomes]
rs10478599	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs10478633	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10515303	0.84[EUR][1000 genomes]
rs11241752	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs11241755	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs11241794	0.83[EUR][1000 genomes]
rs11584	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11738152	0.93[CEU][hapmap];0.96[EUR][1000 genomes]
rs11741369	0.85[EUR][1000 genomes]
rs11742480	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs11742504	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs11748306	0.81[EUR][1000 genomes]
rs12153670	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs12332145	0.85[EUR][1000 genomes]
rs12332642	0.85[EUR][1000 genomes]
rs12719316	0.85[EUR][1000 genomes]
rs13355889	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13357545	0.85[EUR][1000 genomes]
rs13358325	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs13436424	0.85[EUR][1000 genomes]
rs13857	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1423380	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1423384	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1423385	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1428439	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1541676	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs1559058	0.96[EUR][1000 genomes]
rs1559059	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs17723545	0.96[EUR][1000 genomes]
rs17724185	0.95[EUR][1000 genomes]
rs17725452	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs17725678	0.90[EUR][1000 genomes]
rs17726346	0.83[EUR][1000 genomes]
rs17780091	0.94[EUR][1000 genomes]
rs17780273	0.94[EUR][1000 genomes]
rs17780471	0.94[EUR][1000 genomes]
rs17780525	0.96[EUR][1000 genomes]
rs17782041	0.90[EUR][1000 genomes]
rs17782250	0.83[CHB][hapmap];0.82[EUR][1000 genomes]
rs1820150	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1833862	0.83[CEU][hapmap];0.90[EUR][1000 genomes]
rs2059845	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs2059846	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2400313	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2544913	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2548256	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2548257	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2548276	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2548278	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548280	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2725116	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2725124	0.93[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28413976	0.94[EUR][1000 genomes]
rs34564041	0.84[EUR][1000 genomes]
rs3756350	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs3756351	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3756352	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3756353	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756354	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3756355	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776155	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs3776167	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs3776168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3776170	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3776171	1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776174	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3776176	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822366	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs3843478	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs3846627	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs3857365	0.93[EUR][1000 genomes]
rs3909452	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3909453	0.85[EUR][1000 genomes]
rs4702991	0.95[EUR][1000 genomes]
rs4703126	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs4703127	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs4703128	0.92[EUR][1000 genomes]
rs4703130	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4703131	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs55805984	0.83[EUR][1000 genomes]
rs55849330	0.93[EUR][1000 genomes]
rs55861847	0.84[EUR][1000 genomes]
rs55959219	0.90[EUR][1000 genomes]
rs55968003	0.81[EUR][1000 genomes]
rs56752243	0.84[EUR][1000 genomes]
rs59030588	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59490571	0.92[EUR][1000 genomes]
rs60663279	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60853907	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs726971	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs72776700	0.84[EUR][1000 genomes]
rs72778607	0.95[EUR][1000 genomes]
rs72778613	0.94[EUR][1000 genomes]
rs72778620	0.94[EUR][1000 genomes]
rs72778635	0.92[EUR][1000 genomes]
rs72778649	0.83[EUR][1000 genomes]
rs72778650	0.81[EUR][1000 genomes]
rs7447673	0.96[EUR][1000 genomes]
rs7703643	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7737721	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9327319	0.96[EUR][1000 genomes]
rs9327323	0.96[EUR][1000 genomes]
rs9327327	0.96[EUR][1000 genomes]
rs966257	0.92[CEU][hapmap];0.95[EUR][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	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	esv1834675	chr5:100143084-100535029	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv969238	chr5:100174140-100182830	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2548279	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100147600-100218000	Weak transcription	Thymus	Thymus
2	chr5:100147800-100179000	Weak transcription	Fetal Thymus	thymus
3	chr5:100170600-100179000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:100174000-100190600	Weak transcription	Fetal Lung	lung
5	chr5:100174200-100179200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:100174600-100177600	Weak transcription	Dnd41	blood
7	chr5:100175000-100177800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr5:100175200-100177800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:100175400-100177800	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr5:100175400-100178200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:100175800-100177800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:100175800-100177800	Enhancers	NHEK	skin
13	chr5:100175800-100178000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:100175800-100178400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr5:100176000-100177600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr5:100176000-100177600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr5:100176000-100177600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:100176000-100177600	Flanking Active TSS	A549	lung
19	chr5:100176000-100177800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr5:100176000-100177800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr5:100176000-100177800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr5:100176000-100177800	Enhancers	Primary B cells from cord blood	blood
23	chr5:100176000-100177800	Enhancers	HMEC	breast
24	chr5:100176000-100178000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:100176000-100178800	Flanking Active TSS	GM12878-XiMat	blood
26	chr5:100176200-100177600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:100176200-100177800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr5:100176200-100178200	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr5:100176200-100178200	Enhancers	Primary B cells from peripheral blood	blood
30	chr5:100176400-100177600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr5:100176400-100177800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:100176400-100177800	Enhancers	Primary hematopoietic stem cells	blood
33	chr5:100176400-100178400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr5:100176600-100177600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:100176600-100177600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr5:100176600-100177600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr5:100176600-100177600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:100176600-100177600	Enhancers	Placenta	Placenta
39	chr5:100176600-100177800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr5:100176600-100177800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:100176600-100177800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr5:100176600-100177800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:100176600-100177800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr5:100176800-100177600	Enhancers	H1 Cell Line	embryonic stem cell
45	chr5:100176800-100177600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr5:100176800-100177800	Enhancers	Primary T cells fromperipheralblood	blood
47	chr5:100177000-100177600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr5:100177000-100177600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr5:100177000-100177600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:100177000-100177600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links