Variant report

Variant	rs12506098
Chromosome Location	chr4:48594659-48594660
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48592723..48596474-chr4:48596603..48599281,4	K562	blood:
2	chr4:48593211..48596100-chr4:48831975..48834046,2	K562	blood:

Variant related genes	Relation type
ENSG00000109180	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10018344	0.86[EUR][1000 genomes]
rs10029732	0.85[EUR][1000 genomes]
rs10030853	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10031777	0.86[EUR][1000 genomes]
rs10938534	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11728565	0.80[ASN][1000 genomes]
rs11734019	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11933919	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12503599	0.85[EUR][1000 genomes]
rs12645501	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13108474	0.86[EUR][1000 genomes]
rs13127730	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13138269	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13151534	0.81[EUR][1000 genomes]
rs1507862	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1507865	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1702798	0.86[EUR][1000 genomes]
rs1712767	0.84[EUR][1000 genomes]
rs1712768	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1712772	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17575720	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17656010	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17656040	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17656076	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17656094	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1876469	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2089503	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2354348	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28470767	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28733443	0.84[EUR][1000 genomes]
rs2940324	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2945330	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs3107022	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34558821	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34635008	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4536901	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4695391	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59686413	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62311296	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6447640	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6447645	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6447647	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6811148	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6819159	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6829144	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6829716	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6830848	0.81[EUR][1000 genomes]
rs6843340	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6855022	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6856448	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7654770	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7661515	0.86[EUR][1000 genomes]
rs7678379	0.84[EUR][1000 genomes]
rs7679210	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7683398	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7693461	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7697851	0.84[EUR][1000 genomes]
rs776584	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs776588	0.83[EUR][1000 genomes]
rs776590	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs776591	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs776601	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs796555	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs937888	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs937889	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs952289	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9884546	0.86[EUR][1000 genomes];0.89[ASN][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
rs12506098	SLC10A4	cis	lung	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48515800-48625000	Weak transcription	Hela-S3	cervix
2	chr4:48525000-48595600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:48528200-48596000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:48542800-48604400	Weak transcription	A549	lung
5	chr4:48545200-48618200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:48546400-48596400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:48557800-48622400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:48559800-48604400	Weak transcription	HepG2	liver
9	chr4:48561400-48604400	Weak transcription	Stomach Mucosa	stomach
10	chr4:48562600-48596600	Weak transcription	Fetal Brain Male	brain
11	chr4:48562800-48623200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:48563000-48637400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:48573200-48604600	Weak transcription	NHLF	lung
14	chr4:48573200-48605600	Weak transcription	Pancreas	Pancrea
15	chr4:48573200-48605600	Weak transcription	Small Intestine	intestine
16	chr4:48575200-48643000	Weak transcription	HSMMtube	muscle
17	chr4:48578000-48596400	Weak transcription	Osteobl	bone
18	chr4:48578200-48605600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:48578600-48637000	Weak transcription	Esophagus	oesophagus
20	chr4:48579600-48615800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr4:48586000-48602200	Weak transcription	Fetal Intestine Small	intestine
22	chr4:48587000-48596800	Weak transcription	NHDF-Ad	bronchial
23	chr4:48587400-48604600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr4:48588400-48596200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:48588400-48602600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:48588400-48644600	Weak transcription	Colon Smooth Muscle	Colon
27	chr4:48588800-48596800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr4:48588800-48597000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:48588800-48619600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:48589800-48595000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr4:48589800-48595200	Strong transcription	Primary B cells from cord blood	blood
32	chr4:48590000-48597800	Strong transcription	HSMM	muscle
33	chr4:48590200-48614000	Weak transcription	Fetal Kidney	kidney
34	chr4:48590600-48605800	Weak transcription	Colonic Mucosa	Colon
35	chr4:48590600-48606400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:48590600-48627600	Weak transcription	Fetal Brain Female	brain
37	chr4:48590800-48595200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr4:48590800-48605600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:48590800-48605800	Weak transcription	Gastric	stomach
40	chr4:48590800-48619600	Weak transcription	Fetal Stomach	stomach
41	chr4:48590800-48619600	Weak transcription	Lung	lung
42	chr4:48591000-48602000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:48591000-48618600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr4:48591000-48619400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:48591200-48596800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:48591200-48626600	Weak transcription	Ovary	ovary
47	chr4:48591400-48599200	Weak transcription	Brain Germinal Matrix	brain
48	chr4:48591400-48619600	Weak transcription	Fetal Muscle Leg	muscle
49	chr4:48591600-48597000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:48591800-48596200	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links