Variant report

Variant	rs2742239
Chromosome Location	chr10:43621712-43621713
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	chr10:43620062..43622835-chr10:43632716..43635230,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169826	Chromatin interaction
ENSG00000273008	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1059484	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10793422	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10793424	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10793426	0.82[EUR][1000 genomes]
rs10793427	0.81[EUR][1000 genomes]
rs10899778	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10899779	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10899780	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10899781	0.86[EUR][1000 genomes]
rs10899782	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10899786	0.82[EUR][1000 genomes]
rs11238476	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11238479	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11238481	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11238483	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11238485	0.84[EUR][1000 genomes]
rs11238490	0.81[EUR][1000 genomes]
rs11528481	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12220534	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12220560	0.87[EUR][1000 genomes]
rs12268309	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12360493	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12416428	0.88[EUR][1000 genomes]
rs1254958	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1254959	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1254960	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1254962	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1254963	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1254965	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1254967	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1254968	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1270015	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1317214	0.85[EUR][1000 genomes]
rs1800861	0.97[ASN][1000 genomes]
rs1864399	0.92[ASN][1000 genomes]
rs1864400	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1879310	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1915142	0.81[EUR][1000 genomes]
rs2003317	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2075910	0.97[ASN][1000 genomes]
rs2075912	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115817	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2249005	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2257767	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2293020	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2435337	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2435338	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2435339	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2435354	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2435376	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2435377	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2435383	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2435384	0.88[ASN][1000 genomes]
rs2435385	0.88[ASN][1000 genomes]
rs2503848	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2503849	0.88[ASN][1000 genomes]
rs2503860	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2503863	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2503864	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2503881	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2505506	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505511	0.94[ASN][1000 genomes]
rs2505512	0.90[ASN][1000 genomes]
rs2505514	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505553	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2505557	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2565200	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2565201	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742233	0.97[ASN][1000 genomes]
rs2742234	0.97[ASN][1000 genomes]
rs2742235	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2742237	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742240	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2742241	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3004214	0.97[ASN][1000 genomes]
rs4648313	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60845448	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61268333	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61845684	0.82[EUR][1000 genomes]
rs7073849	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7093409	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7096500	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7098236	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7098237	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs715106	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs741968	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs871763	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[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	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	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
5	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
6	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
7	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2742239	CSGALNACT2	cis	Artery Tibial	GTEx
rs2742239	CSGALNACT2	cis	Thyroid	GTEx
rs2742239	CSGALNACT2	cis	Nerve Tibial	GTEx
rs2742239	CSGALNACT2	cis	Heart Left Ventricle	GTEx
rs2742239	CSGALNACT2	cis	lung	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43601400-43632800	Weak transcription	Gastric	stomach
2	chr10:43601600-43624800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr10:43606400-43632600	Weak transcription	Right Atrium	heart
4	chr10:43606600-43626000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr10:43609800-43626800	Weak transcription	Fetal Intestine Small	intestine
6	chr10:43614800-43626800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr10:43617200-43624600	Weak transcription	Fetal Lung	lung
8	chr10:43617200-43632000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr10:43617400-43622000	Weak transcription	HUVEC	blood vessel
10	chr10:43617400-43632200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr10:43617600-43621800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr10:43617600-43623200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr10:43617600-43624400	Weak transcription	Fetal Thymus	thymus
14	chr10:43618000-43621800	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr10:43618000-43622000	Weak transcription	Primary B cells from cord blood	blood
16	chr10:43618000-43622000	Weak transcription	GM12878-XiMat	blood
17	chr10:43618000-43622200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr10:43618000-43632600	Weak transcription	Spleen	Spleen
19	chr10:43618600-43622000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr10:43618800-43622600	Weak transcription	Colonic Mucosa	Colon
21	chr10:43619400-43622200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr10:43619600-43625800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr10:43619800-43622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:43620000-43621800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr10:43620200-43622000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:43620400-43621800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr10:43621000-43622200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr10:43621200-43622000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr10:43621400-43622200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr10:43621600-43621800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr10:43621600-43625400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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