Variant report

Variant	rs1709422
Chromosome Location	chr4:130064878-130064879
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1374491	0.81[YRI][hapmap]
rs1699388	0.84[YRI][hapmap]
rs1699391	0.84[YRI][hapmap]
rs1699393	0.84[YRI][hapmap]
rs1854773	0.83[YRI][hapmap]
rs1854774	0.84[YRI][hapmap]
rs3099899	0.84[YRI][hapmap]
rs3113489	0.85[YRI][hapmap]
rs337263	0.89[YRI][hapmap]
rs337276	0.85[CHB][hapmap]
rs389376	0.89[YRI][hapmap]
rs395864	0.87[YRI][hapmap]
rs4975193	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv511266	chr4:130060230-130072652	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv32610	chr4:130062342-130065491	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3464537	chr4:130064302-130070200	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1709422	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs1709422	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs1709422	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs1709422	C4orf33	cis	Whole Blood	GTEx
rs1709422	C4orf33	cis	Artery Tibial	GTEx
rs1709422	C4orf33	cis	Lymphoblastoid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130060200-130065800	Weak transcription	K562	blood
2	chr4:130060400-130065800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr4:130060400-130066000	Weak transcription	Pancreas	Pancrea
4	chr4:130063200-130065800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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Input of quick search could be:

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

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