Variant report

Variant	rs1712772
Chromosome Location	chr4:48626639-48626640
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48617803..48619987-chr4:48625513..48627565,2	K562	blood:
2	chr4:48626369..48628098-chr4:48781487..48784150,2	MCF-7	breast:
3	chr4:48595665..48598613-chr4:48625026..48627031,2	K562	blood:
4	chr4:48615973..48618309-chr4:48625425..48627835,2	K562	blood:
5	chr4:48572897..48575148-chr4:48625721..48628316,2	K562	blood:

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:83)

rs_ID	r²[population]
rs10018344	0.81[EUR][1000 genomes]
rs10029732	0.80[EUR][1000 genomes]
rs10030853	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10031777	0.81[EUR][1000 genomes]
rs10938534	0.81[EUR][1000 genomes]
rs10938537	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11728565	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11734019	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11737677	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11933919	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11943219	0.81[EUR][1000 genomes]
rs12506098	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12645501	0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13108474	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13127730	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13138269	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13151534	0.81[ASN][1000 genomes]
rs1507862	0.81[EUR][1000 genomes]
rs1507865	0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1702798	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1712767	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1712768	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17575720	0.83[EUR][1000 genomes]
rs17656010	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17656040	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17656076	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17656094	0.80[CEU][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1876469	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2089503	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2102397	0.86[YRI][hapmap]
rs2176460	0.93[YRI][hapmap]
rs2354312	0.82[EUR][1000 genomes]
rs2354348	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2354938	0.93[YRI][hapmap]
rs28470767	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28733443	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2940324	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945330	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3107022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34558821	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34635008	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4536901	0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4695391	0.82[CEU][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4695397	0.84[EUR][1000 genomes]
rs4695400	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4695401	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs59686413	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62311296	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6447640	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6447645	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6447647	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6447655	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6811148	0.94[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6818954	0.82[EUR][1000 genomes]
rs6819159	0.81[EUR][1000 genomes]
rs6829144	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6829716	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6830848	0.80[CEU][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6843340	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6855022	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6856448	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7654770	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7657332	0.86[YRI][hapmap]
rs7657698	0.80[CEU][hapmap];0.94[YRI][hapmap]
rs7661515	0.81[EUR][1000 genomes]
rs7667288	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7679210	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7680280	0.83[EUR][1000 genomes]
rs7681070	0.82[EUR][1000 genomes]
rs7683398	0.82[EUR][1000 genomes]
rs7693461	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7697522	0.94[YRI][hapmap];0.82[EUR][1000 genomes]
rs776584	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs776588	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs776590	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs776591	0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs776601	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs796555	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937888	0.82[CEU][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs937889	0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952289	0.81[EUR][1000 genomes]
rs9790336	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9884546	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
rs1712772	SLC10A4	cis	lung	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48563000-48637400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:48575200-48643000	Weak transcription	HSMMtube	muscle
3	chr4:48578600-48637000	Weak transcription	Esophagus	oesophagus
4	chr4:48588400-48644600	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:48590600-48627600	Weak transcription	Fetal Brain Female	brain
6	chr4:48594000-48637400	Weak transcription	Spleen	Spleen
7	chr4:48597800-48644600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr4:48598200-48634800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:48606000-48626800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:48606800-48637800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:48606800-48645000	Weak transcription	Gastric	stomach
12	chr4:48609800-48637000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:48614400-48628800	Weak transcription	Fetal Kidney	kidney
14	chr4:48614600-48637000	Weak transcription	Small Intestine	intestine
15	chr4:48617800-48627000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:48618200-48627800	Strong transcription	Dnd41	blood
17	chr4:48620200-48626800	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:48620200-48628600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:48620200-48634800	Weak transcription	Aorta	Aorta
20	chr4:48620200-48634800	Weak transcription	Left Ventricle	heart
21	chr4:48620200-48637000	Weak transcription	Fetal Lung	lung
22	chr4:48620200-48637400	Weak transcription	Pancreas	Pancrea
23	chr4:48620200-48644800	Weak transcription	Fetal Stomach	stomach
24	chr4:48620400-48634800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:48620600-48635800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:48621200-48637200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:48621200-48642400	Weak transcription	Fetal Heart	heart
28	chr4:48621200-48729400	Weak transcription	Thymus	Thymus
29	chr4:48621400-48628000	Weak transcription	NH-A	brain
30	chr4:48621600-48634800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:48621800-48635000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:48621800-48637400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr4:48621800-48642200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:48621800-48645000	Weak transcription	Lung	lung
35	chr4:48621800-48655800	Weak transcription	Colonic Mucosa	Colon
36	chr4:48622200-48626800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:48622800-48626800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:48622800-48631800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:48622800-48637000	Weak transcription	Adipose Nuclei	Adipose
40	chr4:48622800-48637600	Weak transcription	Liver	Liver
41	chr4:48622800-48644800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:48622800-48648400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:48623000-48631400	Weak transcription	HUVEC	blood vessel
44	chr4:48623000-48634800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr4:48623000-48635600	Weak transcription	NHDF-Ad	bronchial
46	chr4:48623200-48628600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr4:48623200-48634800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr4:48623200-48637000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:48623200-48637000	Weak transcription	Psoas Muscle	Psoas
50	chr4:48623200-48637000	Weak transcription	GM12878-XiMat	blood

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