Variant report

Variant	rs4695401
Chromosome Location	chr4:48742730-48742731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10003273	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10008265	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11727343	0.81[EUR][1000 genomes]
rs11939889	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11943219	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512637	0.83[EUR][1000 genomes]
rs12641022	0.83[EUR][1000 genomes]
rs13113370	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13119414	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13141838	0.88[EUR][1000 genomes]
rs13142540	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1517674	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1554256	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1554258	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1589107	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1702798	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1712767	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1712772	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1980193	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2056201	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2176460	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2354314	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2572345	0.83[EUR][1000 genomes]
rs2572350	0.81[EUR][1000 genomes]
rs2712156	0.83[EUR][1000 genomes]
rs2712157	0.82[EUR][1000 genomes]
rs2712158	0.83[EUR][1000 genomes]
rs2712159	0.83[EUR][1000 genomes]
rs28733443	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2883562	0.83[EUR][1000 genomes]
rs2940324	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3107022	0.80[AFR][1000 genomes]
rs4694906	0.83[EUR][1000 genomes]
rs4695397	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4695400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57797824	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62309747	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6447651	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6447655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447660	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6814811	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6830078	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6830848	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6853588	0.86[EUR][1000 genomes]
rs7657332	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7657698	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7660206	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7665209	0.83[EUR][1000 genomes]
rs7670939	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7680280	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7681070	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682859	0.87[ASN][1000 genomes]
rs7697522	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs776584	0.80[AFR][1000 genomes]
rs776588	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs796555	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs937889	0.81[EUR][1000 genomes]
rs955683	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9790336	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	esv1792683	chr4:48686817-48764009	Strong transcription Weak transcription Enhancers Active TSS Flanking 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	esv1795181	chr4:48686817-48764009	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	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
11	esv1792281	chr4:48719424-48764009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1794245	chr4:48719424-48764009	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1794757	chr4:48719424-48764009	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4695401	SLC10A4	cis	lung	GTEx
rs4695401	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48730200-48744400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:48731600-48744000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:48731600-48751000	Weak transcription	Lung	lung
4	chr4:48731600-48779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:48738000-48746800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr4:48738200-48745400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr4:48738200-48746600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr4:48738200-48747000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:48739400-48745600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr4:48739400-48747200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr4:48739800-48744000	Weak transcription	Brain Substantia Nigra	brain
12	chr4:48740000-48745200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr4:48740400-48746400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:48740600-48743800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:48740600-48745200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr4:48740800-48743000	Enhancers	Liver	Liver
17	chr4:48740800-48746000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr4:48741000-48751200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:48741200-48744800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:48741400-48743400	Enhancers	GM12878-XiMat	blood
21	chr4:48741400-48745600	Enhancers	Primary T cells from cord blood	blood
22	chr4:48741400-48747000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr4:48741600-48744400	Enhancers	Small Intestine	intestine
24	chr4:48741800-48743200	Enhancers	Primary B cells from peripheral blood	blood
25	chr4:48741800-48743200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:48741800-48745000	Enhancers	Primary hematopoietic stem cells	blood
27	chr4:48742000-48743200	Weak transcription	Psoas Muscle	Psoas
28	chr4:48742000-48743400	Weak transcription	Left Ventricle	heart
29	chr4:48742000-48744000	Weak transcription	Thymus	Thymus
30	chr4:48742000-48744400	Weak transcription	Stomach Mucosa	stomach
31	chr4:48742000-48744600	Enhancers	K562	blood
32	chr4:48742000-48758800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:48742000-48768400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:48742200-48742800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:48742200-48743000	Weak transcription	NHEK	skin
36	chr4:48742200-48744400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr4:48742600-48742800	Enhancers	Brain Cingulate Gyrus	brain
38	chr4:48742600-48742800	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr4:48742600-48742800	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr4:48742600-48743000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:48742600-48743200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:48742600-48743200	Enhancers	Brain Anterior Caudate	brain
43	chr4:48742600-48743200	Enhancers	Brain Hippocampus Middle	brain
44	chr4:48742600-48744000	Weak transcription	Gastric	stomach
45	chr4:48742600-48744800	Enhancers	HUVEC	blood vessel
46	chr4:48742600-48745800	Enhancers	Dnd41	blood
47	chr4:48742600-48751200	Weak transcription	Esophagus	oesophagus
48	chr4:48742600-48768200	Weak transcription	Pancreas	Pancrea

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