Variant report

Variant	rs10899780
Chromosome Location	chr10:43725796-43725797
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr10:43725697-43726136	H1-hESC	embryonic stem cell:	n/a	chr10:43725804-43725816
2	TEAD4	chr10:43725724-43726091	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr10:43725749-43726057	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr10:43725738-43726076	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr10:43725532-43726036	H1-hESC	embryonic stem cell:	n/a	chr10:43725803-43725812 chr10:43725579-43725589
6	MXI1	chr10:43725763-43725908	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF263	chr10:43725565-43725962	HEK293-T-REx	kidney:	n/a	n/a
8	ZNF143	chr10:43725633-43726045	H1-hESC	embryonic stem cell:	n/a	chr10:43725824-43725842
9	JUND	chr10:43725713-43725963	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3A	chr10:43724727-43726034	H1-hESC	embryonic stem cell:	n/a	chr10:43724859-43724872
11	MAX	chr10:43725173-43726037	H1-hESC	embryonic stem cell:	n/a	chr10:43725803-43725812 chr10:43725579-43725589

Variant related genes	Relation type
RASGEF1A	TF binding region

Extended variants
information (count: 101 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1059484	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10793422	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10793424	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10793426	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10793427	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899778	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899779	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899781	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899782	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899786	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899787	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11238476	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11238479	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11238481	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11238483	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11238485	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11238490	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11528481	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12220534	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12220560	0.93[EUR][1000 genomes]
rs12268309	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12356643	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12360493	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12416428	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1254958	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1254959	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1254960	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254962	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254963	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254965	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254967	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1254968	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1270015	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1317214	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1879310	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1915142	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2003317	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2075912	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2115817	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2249005	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2257767	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2293020	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2435337	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2435338	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2435339	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2435354	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2435376	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2435377	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2435383	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2435384	0.91[ASN][1000 genomes]
rs2435385	0.91[ASN][1000 genomes]
rs2460551	0.82[ASN][1000 genomes]
rs2503848	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2503849	0.91[ASN][1000 genomes]
rs2503853	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2503860	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2503863	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2503864	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2503881	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505506	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505511	0.86[ASN][1000 genomes]
rs2505514	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2505534	0.82[ASN][1000 genomes]
rs2505553	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505557	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2565200	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2565201	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2742237	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2742239	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2742240	0.83[ASN][1000 genomes]
rs2742241	0.83[ASN][1000 genomes]
rs3004214	0.83[ASN][1000 genomes]
rs3107331	0.83[ASN][1000 genomes]
rs4648313	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60845448	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61268333	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61845684	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7073849	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7093409	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7096500	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7098236	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7098237	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs715106	0.80[EUR][1000 genomes]
rs741968	0.84[EUR][1000 genomes]
rs871763	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
11	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
12	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
13	nsv825351	chr10:43714249-43788481	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1035873	chr10:43721143-43873664	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv466882	chr10:43721481-43849358	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	nsv550697	chr10:43721481-43849358	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10899780	CSGALNACT2	cis	Heart Left Ventricle	GTEx
rs10899780	CSGALNACT2	cis	Nerve Tibial	GTEx
rs10899780	CSGALNACT2	cis	Thyroid	GTEx
rs10899780	CSGALNACT2	cis	Artery Tibial	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43724000-43725800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
2	chr10:43724000-43726000	Bivalent Enhancer	Fetal Muscle Leg	muscle
3	chr10:43724200-43725800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr10:43724200-43725800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr10:43724400-43725800	Enhancers	Fetal Heart	heart
6	chr10:43724400-43726000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
7	chr10:43724400-43726000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr10:43724400-43726200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr10:43724400-43726200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr10:43724600-43725800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr10:43724600-43725800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr10:43724600-43725800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
13	chr10:43724600-43725800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr10:43724600-43726000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr10:43724600-43726000	Bivalent Enhancer	Liver	Liver
16	chr10:43724600-43726000	Bivalent Enhancer	Fetal Stomach	stomach
17	chr10:43724800-43725800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr10:43724800-43725800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:43724800-43725800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:43724800-43726000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr10:43724800-43726000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr10:43724800-43726000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr10:43724800-43727400	Enhancers	Spleen	Spleen
24	chr10:43724800-43727600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr10:43725000-43726000	Active TSS	Brain Anterior Caudate	brain
26	chr10:43725000-43726200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr10:43725000-43727800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr10:43725200-43725800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
29	chr10:43725200-43726000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
30	chr10:43725200-43726200	Bivalent Enhancer	Adipose Nuclei	Adipose
31	chr10:43725200-43727600	Enhancers	Primary B cells from cord blood	blood
32	chr10:43725200-43727800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:43725200-43727800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr10:43725400-43725800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr10:43725400-43725800	Bivalent/Poised TSS	Right Ventricle	heart
36	chr10:43725400-43726200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr10:43725400-43726400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
38	chr10:43725400-43726400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr10:43725400-43727000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
40	chr10:43725400-43727400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr10:43725400-43727600	Enhancers	Primary B cells from peripheral blood	blood
42	chr10:43725400-43727800	Enhancers	Primary hematopoietic stem cells	blood
43	chr10:43725400-43727800	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr10:43725600-43725800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr10:43725600-43725800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
46	chr10:43725600-43725800	Bivalent Enhancer	Primary T cells from cord blood	blood
47	chr10:43725600-43725800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr10:43725600-43725800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr10:43725600-43725800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:43725600-43725800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links