Variant report

Variant	rs13119504
Chromosome Location	chr4:48684999-48685000
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48683162..48685673-chr4:48779626..48783041,3	MCF-7	breast:
2	chr4:48684102..48685627-chr4:48698753..48700458,2	K562	blood:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10003273	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10008265	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10018344	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10030853	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10031777	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10049761	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938534	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10938537	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11728565	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11734019	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11737677	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11933919	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12503599	0.83[AMR][1000 genomes]
rs13108474	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13108799	0.86[AMR][1000 genomes]
rs13113370	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13127730	0.83[EUR][1000 genomes]
rs13138269	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13142540	0.83[AMR][1000 genomes]
rs13151534	0.88[AMR][1000 genomes]
rs1507862	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1517674	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1554256	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1554258	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1589107	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1702798	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1712767	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17575720	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1876469	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2056201	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2089503	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2354312	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2354314	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2354348	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28470767	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28733443	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2940324	0.80[EUR][1000 genomes]
rs34558821	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4695397	0.82[EUR][1000 genomes]
rs6447645	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6447647	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6447651	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6447655	0.80[ASN][1000 genomes]
rs6814811	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6818954	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6819159	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6830848	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6843340	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6856448	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7660206	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7661515	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7667288	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7670939	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7679210	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7680280	0.80[ASN][1000 genomes]
rs7682859	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7683398	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7693461	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs776588	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs796555	0.80[EUR][1000 genomes]
rs937889	0.81[EUR][1000 genomes]
rs952289	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs955683	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9790336	0.80[ASN][1000 genomes]
rs9884546	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv999203	chr4:48645887-48735512	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1802666	chr4:48646594-48721327	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1013914	chr4:48652784-48728934	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv537090	chr4:48652784-48728934	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13119504	SLC10A4	cis	lung	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
2	chr4:48638400-48686200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:48655800-48685600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr4:48657400-48686000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:48657400-48688600	Weak transcription	Brain Angular Gyrus	brain
6	chr4:48657600-48688600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:48663600-48700200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:48666600-48685600	Weak transcription	Dnd41	blood
9	chr4:48666600-48686800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:48668200-48686200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:48668200-48688000	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:48668200-48689400	Weak transcription	HSMM	muscle
13	chr4:48670000-48691000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr4:48670200-48700000	Weak transcription	Esophagus	oesophagus
15	chr4:48670200-48702000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:48670200-48702000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:48670400-48696000	Weak transcription	Left Ventricle	heart
18	chr4:48671200-48685400	Weak transcription	Fetal Thymus	thymus
19	chr4:48671200-48688600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:48671400-48685800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr4:48671400-48686200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr4:48671400-48686400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr4:48671400-48696000	Weak transcription	Right Ventricle	heart
24	chr4:48671600-48685800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:48672200-48686400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr4:48673000-48686000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:48674800-48689600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:48674800-48689600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:48675000-48685800	Weak transcription	Primary B cells from cord blood	blood
30	chr4:48675000-48688800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:48677000-48686400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:48679000-48700000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:48680200-48685800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr4:48680200-48692800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:48680600-48699600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:48681800-48686200	Weak transcription	Stomach Mucosa	stomach
37	chr4:48683200-48688600	Weak transcription	Brain Anterior Caudate	brain
38	chr4:48683200-48691000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:48683400-48685800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr4:48683400-48685800	Weak transcription	Brain Substantia Nigra	brain
41	chr4:48683400-48685800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr4:48683400-48686400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:48683400-48689600	Weak transcription	Primary T cells from cord blood	blood
44	chr4:48683400-48699600	Weak transcription	Psoas Muscle	Psoas
45	chr4:48683600-48685800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr4:48683600-48685800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr4:48683600-48686000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr4:48683600-48692400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr4:48683600-48700000	Weak transcription	Fetal Intestine Large	intestine
50	chr4:48683600-48700400	Weak transcription	Rectal Mucosa Donor 29	rectum

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