Variant report

Variant	rs1864399
Chromosome Location	chr10:43610455-43610456
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43609230..43611797-chr10:43616396..43619297,2	K562	blood:
2	chr10:43604452..43607562-chr10:43608780..43611078,3	K562	blood:
3	chr10:43607653..43609397-chr10:43610018..43611648,2	MCF-7	breast:
4	chr10:43605967..43607514-chr10:43608103..43610558,2	MCF-7	breast:
5	chr10:43610105..43612462-chr19:13953320..13955874,2	MCF-7	breast:
6	chr10:43607946..43610650-chr10:43632814..43635472,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273008	Chromatin interaction
ENSG00000169826	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1059484	0.81[ASN][1000 genomes]
rs1254959	0.80[ASN][1000 genomes]
rs1254960	0.81[ASN][1000 genomes]
rs1254962	0.81[ASN][1000 genomes]
rs1254963	0.81[ASN][1000 genomes]
rs1254965	0.81[ASN][1000 genomes]
rs1254967	0.81[ASN][1000 genomes]
rs1254968	0.81[ASN][1000 genomes]
rs1270015	0.81[ASN][1000 genomes]
rs1272142	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17153156	0.85[EUR][1000 genomes]
rs1800861	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1864395	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1864400	0.95[ASN][1000 genomes]
rs2003317	0.81[ASN][1000 genomes]
rs2075910	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2075912	0.92[ASN][1000 genomes]
rs2075913	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2115817	0.81[ASN][1000 genomes]
rs2249005	0.89[ASN][1000 genomes]
rs2257767	0.82[ASN][1000 genomes]
rs2293020	0.81[ASN][1000 genomes]
rs2435337	0.82[ASN][1000 genomes]
rs2435338	0.86[ASN][1000 genomes]
rs2435339	0.86[ASN][1000 genomes]
rs2435354	0.82[ASN][1000 genomes]
rs2435377	0.81[ASN][1000 genomes]
rs2435383	0.81[ASN][1000 genomes]
rs2435384	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2435385	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2503841	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2503848	0.81[ASN][1000 genomes]
rs2503849	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2503860	0.81[ASN][1000 genomes]
rs2503863	0.81[ASN][1000 genomes]
rs2503864	0.81[ASN][1000 genomes]
rs2503865	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2503866	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2503881	0.81[ASN][1000 genomes]
rs2505505	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2505506	0.83[ASN][1000 genomes]
rs2505511	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2505512	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505513	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2505514	0.89[ASN][1000 genomes]
rs2505553	0.81[ASN][1000 genomes]
rs2505554	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2565200	0.92[ASN][1000 genomes]
rs2565201	0.92[ASN][1000 genomes]
rs2742233	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742234	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742235	0.90[ASN][1000 genomes]
rs2742237	0.92[ASN][1000 genomes]
rs2742239	0.92[ASN][1000 genomes]
rs2742240	0.89[ASN][1000 genomes]
rs2742241	0.89[ASN][1000 genomes]
rs3004211	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3004214	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs715106	0.94[ASN][1000 genomes]
rs741968	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv1038102	chr10:43441601-43642908	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv466880	chr10:43452436-43616751	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
5	nsv550695	chr10:43452436-43616751	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
6	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1051701	chr10:43555542-43642895	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv522592	chr10:43574936-43615505	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv522566	chr10:43596728-43610671	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv1046892	chr10:43609488-43636278	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1864399	CSGALNACT2	cis	Esophagus Muscularis	GTEx
rs1864399	CSGALNACT2	cis	Skin Sun Exposed Lower leg	GTEx
rs1864399	CSGALNACT2	cis	Artery Tibial	GTEx
rs1864399	CSGALNACT2	cis	Nerve Tibial	GTEx
rs1864399	CSGALNACT2	cis	Esophagus Mucosa	GTEx
rs1864399	CSGALNACT2	cis	Heart Left Ventricle	GTEx
rs1864399	CSGALNACT2	cis	Thyroid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43601400-43613400	Weak transcription	Liver	Liver
2	chr10:43601400-43632800	Weak transcription	Gastric	stomach
3	chr10:43601600-43611200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr10:43601600-43624800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr10:43605400-43611800	Enhancers	Fetal Intestine Large	intestine
6	chr10:43606400-43614800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr10:43606400-43632600	Weak transcription	Right Atrium	heart
8	chr10:43606600-43616400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr10:43606600-43616800	Weak transcription	Right Ventricle	heart
10	chr10:43606600-43626000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:43606800-43616800	Weak transcription	Fetal Lung	lung
12	chr10:43607400-43611200	Weak transcription	Fetal Muscle Leg	muscle
13	chr10:43607800-43617400	Weak transcription	Spleen	Spleen
14	chr10:43609200-43616600	Weak transcription	HUVEC	blood vessel
15	chr10:43609400-43614400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr10:43609400-43614400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr10:43609600-43610800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr10:43609800-43610800	Weak transcription	Placenta	Placenta
19	chr10:43609800-43614200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr10:43609800-43626800	Weak transcription	Fetal Intestine Small	intestine
21	chr10:43610200-43611200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr10:43610400-43615000	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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