Variant report

Variant	rs2613670
Chromosome Location	chr5:7921873-7921874
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	chr5:7921838-7922007	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:7921024..7923404-chr5:7924962..7926484,2	K562	blood:

Variant related genes	Relation type
ENSG00000251168	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs162031	0.91[TSI][hapmap]
rs162032	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs162037	0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs162038	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs162040	0.80[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs162045	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs162048	0.82[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs162051	0.85[ASN][1000 genomes]
rs162130	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs162270	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs162272	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs162273	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16879452	0.99[ASN][1000 genomes]
rs1826541	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994866	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2077744	0.80[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2613663	0.98[ASN][1000 genomes]
rs2624228	0.99[ASN][1000 genomes]
rs2624229	0.99[ASN][1000 genomes]
rs2624230	0.99[ASN][1000 genomes]
rs2624231	0.98[ASN][1000 genomes]
rs2624237	0.85[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2640664	0.99[ASN][1000 genomes]
rs2640665	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326120	0.89[TSI][hapmap]
rs326122	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs326124	0.80[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs326981	0.88[ASN][1000 genomes]
rs327573	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs327575	0.90[JPT][hapmap]
rs327582	0.81[AMR][1000 genomes]
rs327588	0.80[EUR][1000 genomes]
rs49672	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv597005	chr5:7860404-8093077	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv427707	chr5:7866234-7966019	Strong transcription Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv508345	chr5:7890892-7933471	Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	esv1844202	chr5:7917101-7923683	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv1846224	chr5:7917101-7923683	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1847591	chr5:7917101-7923683	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv1850880	chr5:7917101-7923683	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv4706	chr5:7917701-7956246	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2613670	MTRR	cis	lymphoblastoid	seeQTL
rs2613670	PAPD7	cis	cerebellum	SCAN
rs2613670	MTRR	cis	multi-tissue	Pritchard
rs2613670	MTRR	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
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