Variant report

Variant	rs2548256
Chromosome Location	chr5:100148462-100148463
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:100144085..100145969-chr5:100148145..100150652,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10043056	0.86[ASN][1000 genomes]
rs10057237	0.85[EUR][1000 genomes]
rs10058901	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10059846	0.87[ASN][1000 genomes]
rs10059953	0.83[EUR][1000 genomes]
rs10060686	0.83[EUR][1000 genomes]
rs10069305	0.87[ASN][1000 genomes]
rs10075853	0.86[EUR][1000 genomes]
rs10078251	0.85[EUR][1000 genomes]
rs10214216	0.80[EUR][1000 genomes]
rs10477661	0.84[EUR][1000 genomes]
rs10478598	0.86[EUR][1000 genomes]
rs10478599	0.86[EUR][1000 genomes]
rs10478633	0.86[ASN][1000 genomes]
rs10478649	0.84[EUR][1000 genomes]
rs11584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741369	0.85[EUR][1000 genomes]
rs11748306	0.82[EUR][1000 genomes]
rs12332145	0.86[EUR][1000 genomes]
rs12332642	0.86[EUR][1000 genomes]
rs12719316	0.85[EUR][1000 genomes]
rs13355889	0.87[ASN][1000 genomes]
rs13357545	0.86[EUR][1000 genomes]
rs13436424	0.86[EUR][1000 genomes]
rs13857	0.86[EUR][1000 genomes]
rs1423380	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1423384	0.89[ASN][1000 genomes]
rs1423385	0.89[ASN][1000 genomes]
rs1428439	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17726244	0.84[EUR][1000 genomes]
rs17782250	0.81[EUR][1000 genomes]
rs1820150	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2059846	0.91[ASN][1000 genomes]
rs2400313	0.83[ASN][1000 genomes]
rs2544913	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2544920	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2548257	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2548261	0.83[EUR][1000 genomes]
rs2548263	0.92[ASN][1000 genomes]
rs2548264	0.84[EUR][1000 genomes]
rs2548265	0.82[EUR][1000 genomes]
rs2548274	0.84[EUR][1000 genomes]
rs2548276	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548278	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2548279	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2548280	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2725116	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2725124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756351	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3756352	0.86[ASN][1000 genomes]
rs3756353	0.87[ASN][1000 genomes]
rs3756354	0.85[ASN][1000 genomes]
rs3756355	0.87[ASN][1000 genomes]
rs3776155	0.86[EUR][1000 genomes]
rs3776168	0.90[ASN][1000 genomes]
rs3776170	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3776171	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3776174	0.86[ASN][1000 genomes]
rs3776176	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3843478	0.86[EUR][1000 genomes]
rs3846626	0.83[EUR][1000 genomes]
rs3909452	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3909453	0.86[EUR][1000 genomes]
rs4703116	0.83[EUR][1000 genomes]
rs4703130	0.88[ASN][1000 genomes]
rs4703133	0.86[EUR][1000 genomes]
rs55817847	0.81[EUR][1000 genomes]
rs59030588	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60663279	0.87[ASN][1000 genomes]
rs60853907	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6864315	0.83[EUR][1000 genomes]
rs72776700	0.84[EUR][1000 genomes]
rs7703643	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7737721	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[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	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	esv3360282	chr5:100148146-100148464	Strong transcription Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2548256	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100139400-100154400	Weak transcription	Fetal Lung	lung
2	chr5:100139400-100155400	Weak transcription	Placenta	Placenta
3	chr5:100139600-100149200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:100142400-100150000	Strong transcription	Dnd41	blood
5	chr5:100142400-100154000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:100142600-100150000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:100143000-100150000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:100143400-100163200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:100145600-100148600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:100145800-100149200	Weak transcription	Brain Germinal Matrix	brain
11	chr5:100145800-100150800	Weak transcription	Adipose Nuclei	Adipose
12	chr5:100145800-100164000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:100147000-100148600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr5:100147600-100148600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr5:100147600-100149600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:100147600-100162000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:100147600-100163200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr5:100147600-100218000	Weak transcription	Thymus	Thymus
19	chr5:100147800-100149600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr5:100147800-100151400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:100147800-100153400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr5:100147800-100154200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:100147800-100154800	Weak transcription	Primary B cells from cord blood	blood
24	chr5:100147800-100161600	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr5:100147800-100161600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr5:100147800-100161800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr5:100147800-100163000	Weak transcription	Primary T cells from cord blood	blood
28	chr5:100147800-100163200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:100147800-100163800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr5:100147800-100163800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:100147800-100179000	Weak transcription	Fetal Thymus	thymus
32	chr5:100148000-100151600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:100148000-100152400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr5:100148200-100161800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr5:100148200-100163200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr5:100148400-100148800	Enhancers	HUVEC	blood vessel

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