Variant report

Variant	rs2354938
Chromosome Location	chr4:48797056-48797057
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48780865..48784136-chr4:48796375..48799379,4	K562	blood:
2	chr4:48794659..48797818-chr4:48831784..48834674,3	MCF-7	breast:
3	chr4:48780865..48783297-chr4:48796375..48799379,3	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction
ENSG00000109180	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12504699	1.00[YRI][hapmap]
rs12512637	1.00[YRI][hapmap]
rs13141523	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs16861510	0.87[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs1712772	0.93[YRI][hapmap]
rs2102397	0.92[YRI][hapmap]
rs2176460	0.82[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2289065	1.00[YRI][hapmap]
rs2354348	0.80[MKK][hapmap]
rs2354937	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2572345	0.83[MKK][hapmap];1.00[YRI][hapmap]
rs2572350	0.81[MKK][hapmap]
rs2712156	0.83[MKK][hapmap];1.00[YRI][hapmap]
rs2712158	0.82[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap]
rs2883561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4694906	1.00[YRI][hapmap]
rs4695396	0.80[ASN][1000 genomes]
rs4695404	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57797824	0.81[AFR][1000 genomes]
rs62309745	0.80[ASN][1000 genomes]
rs62309751	0.86[ASN][1000 genomes]
rs62310883	0.84[ASN][1000 genomes]
rs6830848	0.92[YRI][hapmap]
rs7657332	0.98[MKK][hapmap];0.93[YRI][hapmap]
rs7657698	1.00[YRI][hapmap]
rs7697522	1.00[YRI][hapmap]
rs776584	1.00[YRI][hapmap]
rs776602	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs796555	0.82[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs937889	0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2354938	OCIAD2	cis	lymphoblastoid	seeQTL
rs2354938	OCIAD2	cis	cerebellum	SCAN
rs2354938	GABRA4	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48789600-48801000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:48791200-48798400	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:48794800-48798400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:48794800-48800000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:48795400-48797200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr4:48796400-48798400	Weak transcription	Brain Substantia Nigra	brain
7	chr4:48796600-48798200	Enhancers	GM12878-XiMat	blood
8	chr4:48796600-48798600	Enhancers	Primary B cells from peripheral blood	blood
9	chr4:48796800-48799000	Enhancers	Primary B cells from cord blood	blood
10	chr4:48797000-48806800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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