Variant report

Variant	rs10478599
Chromosome Location	chr5:100156009-100156010
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:100155753-100156085	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:100149835..100151666-chr5:100153497..100156405,2	MCF-7	breast:
2	chr5:100128599..100130272-chr5:100154288..100156292,2	MCF-7	breast:

Variant related genes	Relation type
MIR548P	TF binding region

Extended variants
information (count: 131 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10043056	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10044903	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10052474	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10057237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10059846	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10069305	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10075853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078251	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10078934	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10463771	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10463772	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10478598	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478633	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10515303	0.88[EUR][1000 genomes]
rs11241752	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11241755	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11241794	0.86[EUR][1000 genomes]
rs11584	0.92[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs11738152	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11741369	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11742480	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11742504	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11745097	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11748306	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153670	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12332145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332642	0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12719316	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13355889	0.88[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13357545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13358325	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13358607	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13360613	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13436424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1423380	0.83[TSI][hapmap]
rs1423384	0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1423385	0.83[EUR][1000 genomes]
rs1428439	0.80[MEX][hapmap];0.83[TSI][hapmap]
rs1541676	0.88[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1559058	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1559059	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs157042	0.80[ASN][1000 genomes]
rs157181	0.80[ASN][1000 genomes]
rs17723545	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17724185	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17725452	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17725678	0.84[EUR][1000 genomes]
rs17726346	0.86[EUR][1000 genomes]
rs17778837	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17780091	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17780273	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17780471	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17780525	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17782041	0.84[EUR][1000 genomes]
rs17782250	0.80[MEX][hapmap];0.83[TSI][hapmap]
rs1833862	0.83[CEU][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs2059845	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2059846	0.84[EUR][1000 genomes]
rs2400313	0.88[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2544920	0.93[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548256	0.86[EUR][1000 genomes]
rs2548257	0.86[EUR][1000 genomes]
rs2548263	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2548278	0.86[GIH][hapmap];0.83[TSI][hapmap]
rs2548279	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs2548280	0.86[EUR][1000 genomes]
rs2725124	0.89[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs276458	0.80[ASN][1000 genomes]
rs276459	0.80[ASN][1000 genomes]
rs276461	0.80[ASN][1000 genomes]
rs277870	0.81[ASN][1000 genomes]
rs28413976	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34564041	0.88[EUR][1000 genomes]
rs3756350	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3756352	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3756353	0.88[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3756354	0.88[CEU][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3756355	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3776155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776167	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3776168	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs3776170	0.83[TSI][hapmap]
rs3776174	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3822366	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3843478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846627	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3857365	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3909452	0.92[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs3909453	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4702990	0.81[EUR][1000 genomes]
rs4702991	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703115	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4703117	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4703118	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4703119	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4703126	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703127	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703128	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4703130	0.82[EUR][1000 genomes]
rs4703131	0.88[CEU][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs55805984	0.86[EUR][1000 genomes]
rs55849330	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55861847	0.88[EUR][1000 genomes]
rs55959219	0.84[EUR][1000 genomes]
rs55968003	0.85[EUR][1000 genomes]
rs56165696	0.81[ASN][1000 genomes]
rs56752243	0.88[EUR][1000 genomes]
rs57055845	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59490571	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60663279	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6886392	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs726971	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72776700	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72778607	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72778613	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72778620	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72778635	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72778649	0.86[EUR][1000 genomes]
rs72778650	0.85[EUR][1000 genomes]
rs7447673	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7721627	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7737721	0.86[GIH][hapmap];0.83[TSI][hapmap]
rs9327319	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9327323	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9327327	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs966257	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9763775	0.81[ASN][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
rs10478599	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 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	chr5:100147600-100162000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:100147600-100163200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:100147600-100218000	Weak transcription	Thymus	Thymus
6	chr5:100147800-100161600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr5:100147800-100161600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr5:100147800-100161800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr5:100147800-100163000	Weak transcription	Primary T cells from cord blood	blood
10	chr5:100147800-100163200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:100147800-100163800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr5:100147800-100163800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:100147800-100179000	Weak transcription	Fetal Thymus	thymus
14	chr5:100148200-100161800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr5:100148200-100163200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:100148600-100173200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr5:100150000-100160400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:100150400-100161200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:100150400-100163400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr5:100152600-100161200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr5:100153400-100158600	Strong transcription	Dnd41	blood
22	chr5:100153800-100163000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr5:100153800-100164000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:100154600-100158000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:100155000-100161800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:100155400-100159200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:100155800-100156400	Weak transcription	GM12878-XiMat	blood
28	chr5:100156000-100160400	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr5:100156000-100163600	Weak transcription	Primary B cells from cord blood	blood

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