Variant report

Variant	rs2249005
Chromosome Location	chr10:43627280-43627281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43616473..43618715-chr10:43626088..43628928,2	MCF-7	breast:
2	chr10:43627150..43629046-chr10:43699034..43700952,2	K562	blood:
3	chr10:43626713..43628248-chr10:43884953..43886619,2	K562	blood:
4	chr10:43626673..43631547-chr10:43631796..43635248,5	K562	blood:

Variant related genes	Relation type
ENSG00000198915	Chromatin interaction
ENSG00000169826	Chromatin interaction
ENSG00000273008	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1059484	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10793422	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10793424	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10793426	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10793427	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10899778	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10899779	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10899780	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10899781	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10899782	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10899786	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11238476	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11238479	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11238481	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11238483	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11238485	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11238490	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11528481	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12220534	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12220560	0.87[EUR][1000 genomes]
rs12268309	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12360493	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12416428	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1254958	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1254959	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1254960	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254962	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254963	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254965	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254967	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254968	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1270015	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1317214	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1800861	0.94[ASN][1000 genomes]
rs1864399	0.89[ASN][1000 genomes]
rs1864400	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1879310	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1915142	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2003317	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2075910	0.94[ASN][1000 genomes]
rs2075912	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2115817	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2257767	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2293020	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2435337	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2435338	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2435339	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2435354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2435376	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2435377	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2435383	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2435384	0.91[ASN][1000 genomes]
rs2435385	0.91[ASN][1000 genomes]
rs2503848	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2503849	0.91[ASN][1000 genomes]
rs2503860	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2503863	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2503864	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2503881	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505506	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505511	0.97[ASN][1000 genomes]
rs2505512	0.92[ASN][1000 genomes]
rs2505514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505553	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505557	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2565200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2565201	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2742233	0.94[ASN][1000 genomes]
rs2742234	0.94[ASN][1000 genomes]
rs2742235	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742237	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2742239	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2742240	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742241	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3004214	1.00[ASN][1000 genomes]
rs4648313	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60845448	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61268333	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61845684	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7073849	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7093409	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7096500	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7098236	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7098237	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs715106	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs741968	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs871763	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[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	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
8	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
9	nsv1042310	chr10:43623060-43688505	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	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
11	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2249005	CSGALNACT2	cis	Nerve Tibial	GTEx
rs2249005	CSGALNACT2	cis	Heart Left Ventricle	GTEx
rs2249005	CSGALNACT2	cis	Thyroid	GTEx
rs2249005	CSGALNACT2	cis	Artery Tibial	GTEx
rs2249005	CSGALNACT2	cis	Adipose Subcutaneous	GTEx
rs2249005	CSGALNACT2	cis	lung	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43601400-43632800	Weak transcription	Gastric	stomach
2	chr10:43606400-43632600	Weak transcription	Right Atrium	heart
3	chr10:43617200-43632000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr10:43617400-43632200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr10:43618000-43632600	Weak transcription	Spleen	Spleen
6	chr10:43621800-43629800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr10:43622800-43632600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:43623400-43632600	Weak transcription	Primary B cells from cord blood	blood
9	chr10:43624800-43631600	Weak transcription	Fetal Muscle Leg	muscle
10	chr10:43624800-43632000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr10:43625000-43629400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:43625000-43631600	Weak transcription	Fetal Lung	lung
13	chr10:43625200-43627600	Enhancers	HSMMtube	muscle
14	chr10:43625200-43632600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr10:43625200-43632600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr10:43625200-43632600	Weak transcription	Thymus	Thymus
17	chr10:43625400-43627400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr10:43625400-43628400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:43625400-43628800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr10:43625400-43628800	Weak transcription	GM12878-XiMat	blood
21	chr10:43625400-43629000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr10:43625400-43631600	Weak transcription	NHLF	lung
23	chr10:43625600-43631200	Weak transcription	Osteobl	bone
24	chr10:43625600-43632000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr10:43625600-43632000	Weak transcription	Fetal Thymus	thymus
26	chr10:43625600-43632000	Weak transcription	HSMM	muscle
27	chr10:43625800-43628200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:43626000-43632400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr10:43626400-43631800	Weak transcription	NHDF-Ad	bronchial
30	chr10:43626400-43632600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr10:43626400-43632600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr10:43626400-43632800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:43626600-43632000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr10:43626600-43632000	Weak transcription	Ovary	ovary
35	chr10:43626800-43627600	Enhancers	Fetal Intestine Small	intestine
36	chr10:43626800-43628200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr10:43626800-43628200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr10:43627000-43632000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr10:43627000-43632200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr10:43627000-43632400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr10:43627200-43627800	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links