Variant report

Variant	rs1957069
Chromosome Location	chr4:74740217-74740218
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	chr4:74717554..74719920-chr4:74738464..74740646,2	K562	blood:

Variant related genes	Relation type
ENSG00000109272	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10007249	0.86[EUR][1000 genomes]
rs10518117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11574452	1.00[CEU][hapmap]
rs12108606	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1435520	1.00[CEU][hapmap]
rs149611	0.89[EUR][1000 genomes]
rs1511815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16845091	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16850160	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16850178	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16850360	0.85[CEU][hapmap]
rs1951233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145614	0.85[CEU][hapmap]
rs2180883	0.85[CEU][hapmap];0.92[GIH][hapmap]
rs2367427	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3111693	0.85[CEU][hapmap];0.92[GIH][hapmap]
rs3117602	0.85[CEU][hapmap]
rs352036	0.89[EUR][1000 genomes]
rs353028	0.89[EUR][1000 genomes]
rs353029	0.83[EUR][1000 genomes]
rs353031	0.86[EUR][1000 genomes]
rs353034	0.86[EUR][1000 genomes]
rs353039	0.86[EUR][1000 genomes]
rs353040	0.86[EUR][1000 genomes]
rs353042	1.00[CEU][hapmap]
rs3756074	1.00[CEU][hapmap]
rs499141	0.86[EUR][1000 genomes]
rs529312	0.86[EUR][1000 genomes]
rs57274239	0.89[EUR][1000 genomes]
rs58324794	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58463118	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs585778	0.86[EUR][1000 genomes]
rs58610473	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60775930	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61412577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629315	0.86[EUR][1000 genomes]
rs671253	0.93[EUR][1000 genomes]
rs6813952	0.87[CEU][hapmap]
rs7656335	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7666671	0.86[EUR][1000 genomes]
rs938094	0.89[EUR][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	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv432612	chr4:74723372-74774372	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1957069	MTHFD2L	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74736000-74741600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr4:74736800-74740600	Weak transcription	NHDF-Ad	bronchial
3	chr4:74736800-74749000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:74737000-74740600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:74737000-74740800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:74737000-74741600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:74737800-74741000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr4:74738000-74741600	Weak transcription	Fetal Stomach	stomach
9	chr4:74738400-74740800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr4:74739600-74741000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr4:74740200-74740400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:74740200-74742200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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