Variant report

Variant	rs1254962
Chromosome Location	chr10:43696992-43696993
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43696369..43700743-chr10:43891529..43894634,3	K562	blood:
2	chr10:43696835..43700131-chr10:43902185..43905182,4	K562	blood:
3	chr10:43696064..43699246-chr10:43901638..43904576,3	K562	blood:
4	chr10:43682496..43684417-chr10:43696461..43698091,2	K562	blood:

Variant related genes	Relation type
ENSG00000169813	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1059484	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10793424	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10793426	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10793427	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899778	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899779	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899780	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899781	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899782	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899786	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899787	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11238476	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238479	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238481	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11238483	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11238485	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11238490	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11528481	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12220534	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12220560	0.93[EUR][1000 genomes]
rs12268309	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12356643	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12360493	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12416428	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1254958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1254959	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1254960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1254963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1254965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1254967	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1254968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1270015	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317214	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800861	0.86[ASN][1000 genomes]
rs1864399	0.81[ASN][1000 genomes]
rs1864400	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1879310	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1915142	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2003317	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075910	0.86[ASN][1000 genomes]
rs2075912	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2115817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249005	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2257767	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293020	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435337	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2435338	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2435339	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2435354	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2435376	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2435377	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435383	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435384	1.00[ASN][1000 genomes]
rs2435385	1.00[ASN][1000 genomes]
rs2503848	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2503849	1.00[ASN][1000 genomes]
rs2503853	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2503860	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2503863	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2503864	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2503881	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505506	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505511	0.94[ASN][1000 genomes]
rs2505512	0.84[ASN][1000 genomes]
rs2505514	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505557	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2565200	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2565201	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2742233	0.86[ASN][1000 genomes]
rs2742234	0.86[ASN][1000 genomes]
rs2742235	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2742237	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2742239	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2742240	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2742241	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3004214	0.91[ASN][1000 genomes]
rs4648313	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60845448	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61268333	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61845684	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7073849	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7093409	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7096500	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7098236	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7098237	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs715106	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs741968	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs871763	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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	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	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
4	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
5	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1831010	chr10:43674916-43759185	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv895084	chr10:43688505-43765485	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv3424466	chr10:43694496-43697294	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv466881	chr10:43695049-43799588	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv550696	chr10:43695049-43799588	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv895085	chr10:43695049-43804617	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1254962	CSGALNACT2	cis	Thyroid	GTEx
rs1254962	CSGALNACT2	cis	lung	GTEx
rs1254962	CSGALNACT2	cis	Adipose Subcutaneous	GTEx
rs1254962	CSGALNACT2	cis	Artery Tibial	GTEx
rs1254962	CSGALNACT2	cis	Nerve Tibial	GTEx
rs1254962	CSGALNACT2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43652600-43697200	Weak transcription	Pancreas	Pancrea
2	chr10:43662200-43697600	Weak transcription	NHEK	skin
3	chr10:43674400-43697800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr10:43675600-43700600	Weak transcription	A549	lung
5	chr10:43675800-43697000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:43679400-43697400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr10:43680000-43697600	Weak transcription	NH-A	brain
8	chr10:43682000-43697400	Weak transcription	Liver	Liver
9	chr10:43682600-43697400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr10:43682600-43697400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr10:43683000-43697000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr10:43683000-43697200	Weak transcription	Primary B cells from cord blood	blood
13	chr10:43683000-43697400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr10:43683000-43697400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr10:43683000-43697400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr10:43683200-43697000	Weak transcription	Fetal Brain Male	brain
17	chr10:43683200-43697200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr10:43683200-43697200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr10:43683400-43697000	Weak transcription	Fetal Intestine Small	intestine
20	chr10:43683800-43697000	Weak transcription	Fetal Lung	lung
21	chr10:43684400-43697200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr10:43684400-43697200	Weak transcription	Ovary	ovary
23	chr10:43684400-43697400	Weak transcription	Primary T cells from cord blood	blood
24	chr10:43686800-43697000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr10:43688600-43697000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr10:43688600-43697800	Weak transcription	Aorta	Aorta
27	chr10:43688800-43697600	Weak transcription	NHLF	lung
28	chr10:43689000-43697800	Weak transcription	HSMM	muscle
29	chr10:43689200-43697200	Weak transcription	Thymus	Thymus
30	chr10:43689200-43697400	Weak transcription	Esophagus	oesophagus
31	chr10:43690000-43697000	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr10:43690000-43697400	Weak transcription	Fetal Brain Female	brain
33	chr10:43690600-43697400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr10:43692000-43697200	Strong transcription	Brain Anterior Caudate	brain
35	chr10:43693400-43697400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr10:43693800-43697200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr10:43694000-43697400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr10:43694600-43697400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr10:43695200-43697600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr10:43695800-43697200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr10:43696000-43697000	Weak transcription	Spleen	Spleen
42	chr10:43696000-43697200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr10:43696000-43697200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr10:43696000-43697200	Weak transcription	Brain Angular Gyrus	brain
45	chr10:43696000-43697200	Weak transcription	Brain Germinal Matrix	brain
46	chr10:43696200-43697000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr10:43696200-43697200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr10:43696200-43697200	Weak transcription	Gastric	stomach
49	chr10:43696200-43697400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr10:43696200-43697400	Weak transcription	Right Atrium	heart

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