Variant report

Variant	rs17752262
Chromosome Location	chr14:78119369-78119370
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	chr14:78081876..78084095-chr14:78119324..78121053,2	MCF-7	breast:
2	chr14:78116603..78122891-chr14:78172785..78176058,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALKBH1-2	chr14:78119170-78119398	NONHSAT037995

Variant related genes	Relation type
ENSG00000100596	Chromatin interaction
ENSG00000119705	Chromatin interaction
ENSG00000100601	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10132900	1.00[JPT][hapmap]
rs10143701	1.00[JPT][hapmap]
rs11621162	0.82[JPT][hapmap]
rs12431525	0.81[ASN][1000 genomes]
rs12431896	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12433954	0.81[ASN][1000 genomes]
rs12434701	0.87[AMR][1000 genomes]
rs12436803	0.81[ASN][1000 genomes]
rs176908	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap]
rs17751917	1.00[CHB][hapmap]
rs17751980	1.00[CHB][hapmap]
rs17751993	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17752428	1.00[JPT][hapmap]
rs17752707	1.00[JPT][hapmap]
rs17752950	1.00[JPT][hapmap]
rs17824984	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17825014	1.00[CHB][hapmap]
rs17825229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17825235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364578	1.00[CHB][hapmap]
rs2886122	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2886132	1.00[CHB][hapmap]
rs35389286	0.81[ASN][1000 genomes]
rs4497612	1.00[CHB][hapmap]
rs55799811	0.81[ASN][1000 genomes]
rs58312042	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59721556	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2758362	chr14:78074180-78262572	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2759998	chr14:78074180-78262572	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv2757575	chr14:78104897-78212462	Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34940	chr14:78104897-78222798	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv521287	chr14:78108003-78211225	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv9155	chr14:78118162-78133830	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17752262	SPTLC2	cis	Nerve Tibial	GTEx
rs17752262	ADCK1	cis	Whole Blood	GTEx
rs17752262	PRKAR1B	trans	cerebellum	SCAN
rs17752262	ADCK1	cis	multi-tissue	Pritchard

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78115400-78120000	Weak transcription	Fetal Intestine Large	intestine
2	chr14:78115600-78120000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr14:78115600-78120800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr14:78116000-78119800	Weak transcription	Adipose Nuclei	Adipose
5	chr14:78118400-78120200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr14:78118600-78119800	Enhancers	HepG2	liver

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