Variant report

Variant	rs1877836
Chromosome Location	chr4:130074764-130074765
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:130012024..130014781-chr4:130073486..130075302,2	K562	blood:
2	chr4:130071377..130073525-chr4:130073844..130076001,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151466	Chromatin interaction
ENSG00000151470	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1030830	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap]
rs10494317	0.80[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs12500557	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12503465	0.89[JPT][hapmap]
rs12504200	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap]
rs12505207	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12512345	0.81[YRI][hapmap]
rs12512846	0.91[ASN][1000 genomes]
rs1376202	0.81[YRI][hapmap]
rs17185550	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17185620	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17416188	0.81[YRI][hapmap]
rs17416706	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap]
rs1900397	0.80[GIH][hapmap];0.81[YRI][hapmap]
rs2044523	0.81[CHB][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap]
rs2597837	0.81[YRI][hapmap]
rs280601	0.81[YRI][hapmap]
rs35162842	0.93[ASN][1000 genomes]
rs4533782	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4635829	0.89[ASN][1000 genomes]
rs4975294	0.85[JPT][hapmap];0.81[YRI][hapmap]
rs4975302	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4975303	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4975304	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4975305	0.92[ASN][1000 genomes]
rs6838427	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6847784	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs72685402	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72687104	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs921375	0.84[JPT][hapmap]
rs921377	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2762460	chr4:130067546-130074947	Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv32740	chr4:130074483-130080201	Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1877836	LOC132321	cis	multi-tissue	Pritchard
rs1877836	FLJ30655	cis	multi-tissue	Pritchard
rs1877836	HSPA4L	cis	parietal	SCAN
rs1877836	ADRB3	trans	cerebellum	SCAN
rs1877836	PHF17	cis	multi-tissue	Pritchard

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

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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