Variant report

Variant	rs2548257
Chromosome Location	chr5:100162317-100162318
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	chr5:100160740..100162427-chr5:100234185..100236458,2	K562	blood:
2	chr5:100157247..100161325-chr5:100161571..100164994,4	MCF-7	breast:

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10043056	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10044903	0.93[EUR][1000 genomes]
rs10052474	0.96[EUR][1000 genomes]
rs10057237	0.86[EUR][1000 genomes]
rs10058901	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10059846	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10069305	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10075853	0.86[EUR][1000 genomes]
rs10078251	0.85[EUR][1000 genomes]
rs10078934	0.95[EUR][1000 genomes]
rs10214216	0.80[EUR][1000 genomes]
rs10463771	0.95[EUR][1000 genomes]
rs10463772	0.95[EUR][1000 genomes]
rs10478598	0.86[EUR][1000 genomes]
rs10478599	0.86[EUR][1000 genomes]
rs10478633	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10515303	0.83[EUR][1000 genomes]
rs11241752	0.90[EUR][1000 genomes]
rs11241755	0.90[EUR][1000 genomes]
rs11241794	0.81[EUR][1000 genomes]
rs11584	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11738152	0.95[EUR][1000 genomes]
rs11741369	0.86[EUR][1000 genomes]
rs11742480	0.93[EUR][1000 genomes]
rs11742504	0.93[EUR][1000 genomes]
rs11748306	0.82[EUR][1000 genomes]
rs12153670	0.95[EUR][1000 genomes]
rs12332145	0.86[EUR][1000 genomes]
rs12332642	0.86[EUR][1000 genomes]
rs12719316	0.86[EUR][1000 genomes]
rs13355889	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13357545	0.86[EUR][1000 genomes]
rs13358325	0.95[EUR][1000 genomes]
rs13436424	0.86[EUR][1000 genomes]
rs13857	0.86[EUR][1000 genomes]
rs1423380	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1423384	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1423385	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1428439	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1541676	0.89[EUR][1000 genomes]
rs1559058	0.95[EUR][1000 genomes]
rs1559059	0.94[EUR][1000 genomes]
rs17723545	0.95[EUR][1000 genomes]
rs17724185	0.94[EUR][1000 genomes]
rs17725452	0.90[EUR][1000 genomes]
rs17725678	0.89[EUR][1000 genomes]
rs17726346	0.81[EUR][1000 genomes]
rs17780091	0.93[EUR][1000 genomes]
rs17780273	0.93[EUR][1000 genomes]
rs17780471	0.93[EUR][1000 genomes]
rs17780525	0.95[EUR][1000 genomes]
rs17782041	0.89[EUR][1000 genomes]
rs17782250	0.81[EUR][1000 genomes]
rs1820150	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1833862	0.89[EUR][1000 genomes]
rs2059845	0.92[EUR][1000 genomes]
rs2059846	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2400313	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2544913	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2544920	0.81[EUR][1000 genomes]
rs2548256	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2548263	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2548276	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2548278	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548279	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2548280	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2725116	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2725124	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28413976	0.93[EUR][1000 genomes]
rs34564041	0.83[EUR][1000 genomes]
rs3756350	0.94[EUR][1000 genomes]
rs3756351	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3756352	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3756353	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756354	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3756355	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776155	0.86[EUR][1000 genomes]
rs3776167	0.93[EUR][1000 genomes]
rs3776168	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776170	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776171	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776174	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3776176	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822366	0.94[EUR][1000 genomes]
rs3843478	0.86[EUR][1000 genomes]
rs3846627	0.92[EUR][1000 genomes]
rs3857365	0.92[EUR][1000 genomes]
rs3909452	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3909453	0.86[EUR][1000 genomes]
rs4702991	0.93[EUR][1000 genomes]
rs4703126	0.93[EUR][1000 genomes]
rs4703127	0.95[EUR][1000 genomes]
rs4703128	0.91[EUR][1000 genomes]
rs4703130	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4703131	0.89[EUR][1000 genomes]
rs55805984	0.81[EUR][1000 genomes]
rs55849330	0.92[EUR][1000 genomes]
rs55861847	0.83[EUR][1000 genomes]
rs55959219	0.89[EUR][1000 genomes]
rs55968003	0.80[EUR][1000 genomes]
rs56752243	0.83[EUR][1000 genomes]
rs59030588	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59490571	0.91[EUR][1000 genomes]
rs60663279	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60853907	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs726971	0.93[EUR][1000 genomes]
rs72776700	0.85[EUR][1000 genomes]
rs72778607	0.94[EUR][1000 genomes]
rs72778613	0.93[EUR][1000 genomes]
rs72778620	0.93[EUR][1000 genomes]
rs72778635	0.91[EUR][1000 genomes]
rs72778649	0.81[EUR][1000 genomes]
rs72778650	0.80[EUR][1000 genomes]
rs7447673	0.95[EUR][1000 genomes]
rs7703643	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7737721	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9327319	0.95[EUR][1000 genomes]
rs9327323	0.95[EUR][1000 genomes]
rs9327327	0.95[EUR][1000 genomes]
rs966257	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2548257	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100143400-100163200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr5:100145800-100164000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr5:100147600-100163200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr5:100147600-100218000	Weak transcription	Thymus	Thymus
5	chr5:100147800-100163000	Weak transcription	Primary T cells from cord blood	blood
6	chr5:100147800-100163200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:100147800-100163800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr5:100147800-100163800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:100147800-100179000	Weak transcription	Fetal Thymus	thymus
10	chr5:100148200-100163200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:100148600-100173200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:100150400-100163400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr5:100153800-100163000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr5:100153800-100164000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:100156000-100163600	Weak transcription	Primary B cells from cord blood	blood
16	chr5:100157400-100163400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:100159000-100163200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:100159200-100163000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:100159200-100163200	Weak transcription	Placenta	Placenta
20	chr5:100159400-100163000	Weak transcription	A549	lung
21	chr5:100159800-100164200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:100159800-100170800	Strong transcription	Dnd41	blood
23	chr5:100160200-100163200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:100160200-100163400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:100160800-100163200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:100161000-100165000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr5:100161200-100162400	Flanking Active TSS	GM12878-XiMat	blood
28	chr5:100161200-100164400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:100161200-100165000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr5:100161200-100165000	Enhancers	HSMM	muscle
31	chr5:100161400-100164400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr5:100161600-100163000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr5:100161600-100165000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:100161800-100162400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr5:100161800-100162400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:100161800-100162400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:100161800-100162400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr5:100161800-100165200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr5:100162000-100163000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr5:100162000-100163200	Weak transcription	Fetal Muscle Leg	muscle
41	chr5:100162000-100165200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:100162200-100163400	Weak transcription	Small Intestine	intestine
43	chr5:100162200-100163800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr5:100162200-100165000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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