Variant report

Variant	rs34498
Chromosome Location	chr5:98296394-98296395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98263389..98266145-chr5:98295951..98300561,6	K562	blood:
2	chr5:98263064..98266794-chr5:98295400..98300838,7	K562	blood:

Variant related genes	Relation type
ENSG00000248489	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10040066	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10041261	0.81[EUR][1000 genomes]
rs10050804	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10479348	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11242567	1.00[CHB][hapmap]
rs11242574	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11745405	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12515042	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13179812	1.00[CHB][hapmap]
rs1472622	1.00[CHB][hapmap]
rs150935	0.82[YRI][hapmap]
rs151102	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1604450	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs161729	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs161730	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs161731	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs161732	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs161739	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs161746	0.82[YRI][hapmap]
rs161750	0.82[YRI][hapmap]
rs161935	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs161936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs161940	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs161947	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs162337	1.00[ASN][1000 genomes]
rs167798	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1875529	1.00[CHB][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs2221268	1.00[CHB][hapmap];0.90[MEX][hapmap];0.81[EUR][1000 genomes]
rs2447826	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs246251	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2545680	0.82[YRI][hapmap]
rs2545735	0.82[YRI][hapmap]
rs2578576	0.82[YRI][hapmap]
rs2578577	0.82[YRI][hapmap]
rs2662256	0.82[YRI][hapmap]
rs325195	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs325199	0.82[YRI][hapmap]
rs325203	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs325204	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs325208	0.82[YRI][hapmap]
rs325220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs326480	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs326481	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326482	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs331542	0.82[YRI][hapmap]
rs34488	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34489	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs34496	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34499	1.00[ASN][1000 genomes]
rs366353	1.00[CHB][hapmap]
rs39660	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs428836	1.00[ASN][1000 genomes]
rs4343864	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4565239	1.00[CHB][hapmap]
rs4583911	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs467728	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[ASN][1000 genomes]
rs469018	1.00[ASN][1000 genomes]
rs4703345	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs539024	1.00[CHB][hapmap]
rs6878136	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs709386	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs709387	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs709388	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs709389	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7449447	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7712408	0.81[EUR][1000 genomes]
rs7719562	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7719649	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7723242	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs819227	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs819230	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs819231	0.87[AMR][1000 genomes];0.91[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	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv537819	chr5:98253348-98299646	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34498	SLCO4C1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98274800-98297200	Weak transcription	Thymus	Thymus
2	chr5:98278600-98299400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr5:98279400-98298400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:98290600-98296800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:98294800-98297200	Enhancers	K562	blood
6	chr5:98295000-98296800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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