Variant report

Variant	rs13146034
Chromosome Location	chr4:48909679-48909680
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48907349..48910637-chr4:48932106..48935377,4	MCF-7	breast:
2	chr4:48907758..48909914-chr4:48938093..48940676,2	MCF-7	breast:
3	chr4:48779823..48782624-chr4:48905090..48909886,4	MCF-7	breast:
4	chr4:48832331..48834187-chr4:48907329..48910001,2	MCF-7	breast:
5	chr4:48831616..48834377-chr4:48906971..48910422,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252913	Chromatin interaction
ENSG00000075539	Chromatin interaction
ENSG00000251334	Chromatin interaction
ENSG00000109180	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10517231	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11734191	0.80[ASN][1000 genomes]
rs11737706	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13152270	0.81[ASN][1000 genomes]
rs1455940	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1463365	0.89[ASN][1000 genomes]
rs2085292	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289065	0.89[ASN][1000 genomes]
rs2290516	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34730980	0.89[ASN][1000 genomes]
rs6447670	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs724598	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7672280	0.83[EUR][1000 genomes]
rs7685360	0.85[ASN][1000 genomes]
rs7687992	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
8	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
9	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
10	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
11	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
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13146034	SLC10A4	cis	lung	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48909000-48910000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:48909000-48911000	Weak transcription	NHDF-Ad	bronchial
3	chr4:48909000-48911000	Weak transcription	NHLF	lung
4	chr4:48909000-48911200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:48909000-48911200	Weak transcription	HSMM	muscle
6	chr4:48909000-48911200	Weak transcription	HSMMtube	muscle
7	chr4:48909000-48911400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:48909200-48910000	Enhancers	Brain Cingulate Gyrus	brain
9	chr4:48909200-48910000	Enhancers	Brain Substantia Nigra	brain
10	chr4:48909200-48910200	Weak transcription	Esophagus	oesophagus
11	chr4:48909200-48910200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:48909200-48910200	Weak transcription	HMEC	breast
13	chr4:48909200-48910400	Weak transcription	NHEK	skin
14	chr4:48909200-48910800	Weak transcription	NH-A	brain
15	chr4:48909200-48911000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:48909200-48911000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:48909200-48911000	Weak transcription	Osteobl	bone
18	chr4:48909200-48911200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:48909200-48911400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:48909200-48911400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:48909200-48911600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr4:48909200-48911600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:48909200-48911600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:48909200-48914800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:48909200-48916200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:48909400-48909800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:48909400-48910000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:48909400-48910800	Enhancers	Stomach Mucosa	stomach
29	chr4:48909400-48911000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:48909400-48911000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:48909400-48911000	Weak transcription	Hela-S3	cervix
32	chr4:48909400-48911000	Weak transcription	HUVEC	blood vessel
33	chr4:48909400-48911200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:48909400-48911200	Weak transcription	A549	lung
35	chr4:48909400-48914600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr4:48909400-48917200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:48909600-48910000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:48909600-48911800	Weak transcription	Primary T cells from cord blood	blood

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