Variant report

Variant	rs34558821
Chromosome Location	chr4:48588742-48588743
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	chr4:48586327..48590238-chr4:48780231..48783624,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10003273	0.81[AMR][1000 genomes]
rs10008265	0.81[AMR][1000 genomes]
rs10018344	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10029732	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10030853	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10031777	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10049761	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10938534	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10938537	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11728565	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11734019	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737677	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11933919	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11945562	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12503599	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12506098	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12645501	0.85[EUR][1000 genomes]
rs13108474	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13113370	0.83[EUR][1000 genomes]
rs13119504	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13127730	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13138269	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13151534	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1507862	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1507865	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1554258	0.81[AMR][1000 genomes]
rs1712768	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1712772	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17575720	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17656010	0.84[ASN][1000 genomes]
rs17656040	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17656076	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17656094	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1876469	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2089503	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292231	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2354312	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2354348	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28470767	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2940324	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2945330	0.86[EUR][1000 genomes]
rs3107022	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34635008	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4536901	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4695391	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59686413	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62311296	0.88[EUR][1000 genomes]
rs6447640	0.86[EUR][1000 genomes]
rs6447645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447647	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447651	0.83[EUR][1000 genomes]
rs6811148	0.87[EUR][1000 genomes]
rs6814811	0.81[AMR][1000 genomes]
rs6818954	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6819159	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6829716	0.86[EUR][1000 genomes]
rs6836632	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6843340	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6855022	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6856448	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7654770	0.86[EUR][1000 genomes]
rs7661515	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7667288	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7670939	0.83[EUR][1000 genomes]
rs7678379	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7679210	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7682859	0.82[EUR][1000 genomes]
rs7683398	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7693461	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7697851	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs776584	0.81[ASN][1000 genomes]
rs776590	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs776591	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs776601	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs796555	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs937888	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs937889	0.81[EUR][1000 genomes]
rs952289	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9884546	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs992423	0.86[AMR][1000 genomes];0.88[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	nsv470034	chr4:48427773-48605628	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv594121	chr4:48427773-48605628	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv829925	chr4:48467693-48639342	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv966557	chr4:48577320-48618907	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	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
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34558821	SLC10A4	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48498600-48593000	Strong transcription	Rectal Mucosa Donor 31	rectum
2	chr4:48499000-48589400	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr4:48500200-48588800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:48515800-48625000	Weak transcription	Hela-S3	cervix
5	chr4:48525000-48595600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:48528200-48596000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:48541200-48594000	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr4:48542800-48604400	Weak transcription	A549	lung
9	chr4:48545200-48618200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:48546400-48596400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:48547400-48593600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:48557800-48622400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:48559800-48604400	Weak transcription	HepG2	liver
14	chr4:48561400-48604400	Weak transcription	Stomach Mucosa	stomach
15	chr4:48562600-48596600	Weak transcription	Fetal Brain Male	brain
16	chr4:48562800-48590400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:48562800-48623200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:48563000-48637400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:48563400-48593600	Weak transcription	Spleen	Spleen
20	chr4:48573200-48590000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:48573200-48604600	Weak transcription	NHLF	lung
22	chr4:48573200-48605600	Weak transcription	Pancreas	Pancrea
23	chr4:48573200-48605600	Weak transcription	Small Intestine	intestine
24	chr4:48573800-48590000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:48575000-48590000	Weak transcription	Right Ventricle	heart
26	chr4:48575000-48590400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:48575200-48643000	Weak transcription	HSMMtube	muscle
28	chr4:48576400-48589000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:48578000-48596400	Weak transcription	Osteobl	bone
30	chr4:48578200-48605600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:48578400-48590000	Weak transcription	Lung	lung
32	chr4:48578600-48590000	Weak transcription	Aorta	Aorta
33	chr4:48578600-48590000	Weak transcription	Gastric	stomach
34	chr4:48578600-48637000	Weak transcription	Esophagus	oesophagus
35	chr4:48579600-48615800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:48580200-48593800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:48582000-48588800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr4:48582000-48589000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:48582200-48589000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr4:48582200-48589000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr4:48582200-48589000	Strong transcription	Fetal Thymus	thymus
42	chr4:48582200-48592200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:48582200-48594400	Strong transcription	Dnd41	blood
44	chr4:48582400-48588800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:48582400-48593800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:48582400-48594400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr4:48582800-48588800	Strong transcription	HSMM	muscle
48	chr4:48582800-48589000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:48583000-48589000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr4:48583200-48590800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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