Variant report

Variant	rs13141523
Chromosome Location	chr4:48789269-48789270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48783390..48785837-chr4:48789039..48791747,3	K562	blood:
2	chr4:48780486..48785837-chr4:48787089..48791393,6	K562	blood:
3	chr4:48784590..48786986-chr4:48788593..48791116,3	MCF-7	breast:
4	chr4:48782469..48785403-chr4:48787452..48790375,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12512637	0.83[CEU][hapmap]
rs13119414	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16861510	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2176460	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2354348	0.95[MKK][hapmap];0.80[YRI][hapmap]
rs2354937	0.99[ASN][1000 genomes]
rs2354938	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[ASN][1000 genomes]
rs2572345	0.84[CEU][hapmap]
rs2572350	0.88[CEU][hapmap]
rs2712156	0.84[CEU][hapmap]
rs2712158	0.84[CEU][hapmap]
rs2883561	0.98[ASN][1000 genomes]
rs4694906	0.84[CEU][hapmap]
rs4695396	0.80[ASN][1000 genomes]
rs4695404	0.94[ASN][1000 genomes]
rs57797824	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62309745	0.80[ASN][1000 genomes]
rs62309751	0.86[ASN][1000 genomes]
rs62310883	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6830078	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6843340	0.86[MKK][hapmap];0.80[YRI][hapmap]
rs7657332	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7665209	0.84[CEU][hapmap]
rs7697522	0.81[CEU][hapmap]
rs776591	0.81[CEU][hapmap]
rs776602	0.85[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs796555	0.81[CEU][hapmap]
rs937889	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13141523	SLC10A4	cis	lung	GTEx
rs13141523	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48783600-48789800	Weak transcription	Brain Anterior Caudate	brain
2	chr4:48783800-48789800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:48786600-48791200	Enhancers	Brain Cingulate Gyrus	brain
4	chr4:48788200-48791200	Enhancers	Brain Hippocampus Middle	brain
5	chr4:48788600-48789600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:48788600-48790000	Enhancers	Fetal Lung	lung
7	chr4:48788600-48790200	Enhancers	Fetal Stomach	stomach
8	chr4:48788800-48789400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:48788800-48790000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:48789000-48789600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr4:48789000-48789600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:48789000-48790000	Weak transcription	Brain Angular Gyrus	brain
13	chr4:48789200-48789400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:48789200-48789600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr4:48789200-48789600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:48789200-48789600	Weak transcription	Brain Substantia Nigra	brain
17	chr4:48789200-48790200	Weak transcription	Fetal Kidney	kidney

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