Variant report

Variant	rs1806961
Chromosome Location	chr15:40768139-40768140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40743916..40746207-chr15:40767844..40769362,2	K562	blood:
2	chr15:40764613..40768482-chr15:40771207..40776375,6	K562	blood:
3	chr15:40743208..40745711-chr15:40766264..40768804,2	MCF-7	breast:
4	chr15:40765795..40768318-chr15:40771145..40773484,3	MCF-7	breast:
5	chr15:40761851..40766417-chr15:40767472..40770724,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169105	Chromatin interaction
ENSG00000244251	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11070275	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11070277	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11632061	0.81[EUR][1000 genomes]
rs11632370	0.81[EUR][1000 genomes]
rs11638742	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11639464	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12594548	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12595610	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12916042	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1811513	0.89[EUR][1000 genomes]
rs1813898	0.81[EUR][1000 genomes]
rs1869301	0.87[EUR][1000 genomes]
rs1869302	0.96[EUR][1000 genomes]
rs1993212	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2034651	0.96[EUR][1000 genomes]
rs2034652	0.96[EUR][1000 genomes]
rs2167795	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412531	0.81[EUR][1000 genomes]
rs2412532	0.81[EUR][1000 genomes]
rs2412534	0.90[EUR][1000 genomes]
rs2444302	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2924386	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2924388	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2959536	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2959545	0.90[EUR][1000 genomes]
rs4923875	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4923876	0.81[EUR][1000 genomes]
rs4924472	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4924478	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924479	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4924480	0.91[EUR][1000 genomes]
rs4924481	0.81[EUR][1000 genomes]
rs588686	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs590046	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603623	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs616937	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs618399	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs619711	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs620198	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6492951	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs654317	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6582	0.81[EUR][1000 genomes]
rs7178756	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7183273	0.88[EUR][1000 genomes]
rs7494968	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8029384	0.81[EUR][1000 genomes]
rs896795	0.81[EUR][1000 genomes]
rs9652415	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs976401	0.90[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	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs1806961	CCDC32	cis	multi-tissue	Pritchard
rs1806961	C15orf57	cis	Nerve Tibial	GTEx
rs1806961	C15orf57	cis	Heart Left Ventricle	GTEx
rs1806961	C15orf57	cis	Muscle Skeletal	GTEx
rs1806961	C15orf57	cis	Adipose Subcutaneous	GTEx
rs1806961	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs1806961	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs1806961	C15orf57	cis	Artery Aorta	GTEx
rs1806961	C15orf57	cis	Esophagus Mucosa	GTEx
rs1806961	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs1806961	RP11-111A22.1	cis	lung	GTEx
rs1806961	RP11-111A22.1	cis	Artery Tibial	GTEx
rs1806961	C15orf57	cis	lung	GTEx
rs1806961	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs1806961	C15orf57	cis	Esophagus Muscularis	GTEx
rs1806961	C15orf57	cis	Artery Tibial	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40763000-40770200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:40764600-40768200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:40764600-40769800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:40764600-40770000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:40764600-40770000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:40764600-40771400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:40764800-40770000	Weak transcription	NHEK	skin
8	chr15:40765000-40769800	Weak transcription	Hela-S3	cervix
9	chr15:40765000-40772400	Weak transcription	Esophagus	oesophagus
10	chr15:40765000-40773400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:40765200-40768400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:40765200-40770200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:40765200-40770800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:40765600-40768400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:40766600-40770000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:40766800-40769800	Weak transcription	K562	blood
17	chr15:40767200-40769000	Weak transcription	Fetal Stomach	stomach
18	chr15:40767400-40769800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:40767600-40771400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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