Variant report

Variant	rs13185915
Chromosome Location	chr5:79905411-79905412
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	chr5:79904526..79908421-chr5:79948729..79951551,3	K562	blood:
2	chr5:79898740..79900890-chr5:79903364..79906205,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228716	Chromatin interaction
ENSG00000113318	Chromatin interaction
ENSG00000251366	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10168	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11951283	1.00[ASN][1000 genomes]
rs11951910	1.00[ASN][1000 genomes]
rs11952744	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1222809	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1232027	0.92[ASN][1000 genomes]
rs13161245	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1346463	0.82[EUR][1000 genomes]
rs1346464	0.82[EUR][1000 genomes]
rs1382539	0.81[EUR][1000 genomes]
rs1382540	0.81[EUR][1000 genomes]
rs1382541	0.81[EUR][1000 genomes]
rs1382542	0.81[EUR][1000 genomes]
rs1478834	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1478835	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1620258	0.82[EUR][1000 genomes]
rs1623489	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1643634	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1643635	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643636	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1643637	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1643638	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1643639	0.81[EUR][1000 genomes]
rs1643641	0.81[EUR][1000 genomes]
rs1643644	0.81[AFR][1000 genomes]
rs1643646	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1643647	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1643648	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1643649	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1643650	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1643651	0.81[EUR][1000 genomes]
rs1643652	0.81[EUR][1000 genomes]
rs1643653	0.80[EUR][1000 genomes]
rs1643655	0.81[EUR][1000 genomes]
rs1643657	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1643658	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1643659	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1643660	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1643661	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1643662	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1643664	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1650648	0.82[EUR][1000 genomes]
rs1650677	0.80[EUR][1000 genomes]
rs1650678	0.80[EUR][1000 genomes]
rs1650679	0.80[EUR][1000 genomes]
rs1650681	0.80[EUR][1000 genomes]
rs1650682	0.80[EUR][1000 genomes]
rs1650688	0.81[EUR][1000 genomes]
rs1650692	0.81[EUR][1000 genomes]
rs1650693	0.81[EUR][1000 genomes]
rs1650696	0.81[EUR][1000 genomes]
rs1650707	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1650709	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1650710	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1650711	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1650712	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1650713	0.82[AFR][1000 genomes]
rs1650715	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1650718	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1650747	0.82[EUR][1000 genomes]
rs1650749	0.82[EUR][1000 genomes]
rs1650750	0.81[EUR][1000 genomes]
rs1677623	0.80[EUR][1000 genomes]
rs1677626	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1677630	0.82[EUR][1000 genomes]
rs1677633	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1677634	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1677636	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1677647	0.81[EUR][1000 genomes]
rs1677652	0.82[EUR][1000 genomes]
rs1677653	0.81[EUR][1000 genomes]
rs1677654	0.82[EUR][1000 genomes]
rs1677655	0.81[EUR][1000 genomes]
rs1677666	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1677667	0.81[EUR][1000 genomes]
rs1677670	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1677680	0.81[EUR][1000 genomes]
rs1677682	0.80[EUR][1000 genomes]
rs1677684	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1677685	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1677686	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1677687	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1677688	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1677689	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1677690	0.80[EUR][1000 genomes]
rs1677691	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1677692	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1677693	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1677694	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1677695	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1677696	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1677698	0.80[EUR][1000 genomes]
rs1677700	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1677701	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1677702	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1677703	0.80[EUR][1000 genomes]
rs1677704	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1677706	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1677707	0.82[EUR][1000 genomes]
rs1677708	0.80[EUR][1000 genomes]
rs1677709	0.82[EUR][1000 genomes]
rs2250063	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2405880	0.81[EUR][1000 genomes]
rs2560423	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2560424	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2618369	0.82[EUR][1000 genomes]
rs2618372	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs56147256	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs56357417	0.80[EUR][1000 genomes]
rs57771284	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs58063248	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs58490646	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs59117994	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs59724253	1.00[ASN][1000 genomes]
rs60186226	1.00[ASN][1000 genomes]
rs60244599	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6151615	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67837398	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs71578847	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs73125358	1.00[ASN][1000 genomes]
rs7387	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs836798	0.82[EUR][1000 genomes]
rs836799	0.82[EUR][1000 genomes]
rs836800	0.82[EUR][1000 genomes]
rs836802	0.82[EUR][1000 genomes]
rs836804	0.82[EUR][1000 genomes]
rs836806	0.82[EUR][1000 genomes]
rs836808	0.82[EUR][1000 genomes]
rs836809	0.82[EUR][1000 genomes]
rs836810	0.82[EUR][1000 genomes]
rs836813	0.82[EUR][1000 genomes]
rs836818	0.86[EUR][1000 genomes]
rs836821	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs836822	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs836823	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs844368	0.81[EUR][1000 genomes]
rs844370	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs857016	0.82[EUR][1000 genomes]
rs861372	0.82[EUR][1000 genomes]
rs861373	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs863215	0.83[EUR][1000 genomes]
rs865645	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs865647	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs966762	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs13185915	DHFR	cis	Muscle Skeletal	GTEx
rs13185915	DHFR	cis	Whole Blood	GTEx
rs13185915	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs13185915	DHFR	cis	Heart Left Ventricle	GTEx
rs13185915	DHFR	cis	Adipose Subcutaneous	GTEx
rs13185915	MSH3	cis	Thyroid	GTEx
rs13185915	MSH3	cis	Whole Blood	GTEx
rs13185915	ANKRD34B	cis	Whole Blood	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79899400-79910200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:79902400-79916600	Weak transcription	Thymus	Thymus
3	chr5:79904000-79905600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr5:79904000-79914400	Weak transcription	Dnd41	blood
5	chr5:79904800-79925000	Weak transcription	Primary B cells from cord blood	blood
6	chr5:79905000-79906600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr5:79905400-79908400	Weak transcription	Monocytes-CD14+_RO01746	blood

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