Variant report

Variant	rs10899787
Chromosome Location	chr10:43750144-43750145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43748329..43751092-chr10:43758387..43762104,3	MCF-7	breast:
2	chr10:43749564..43751225-chr10:43756675..43758831,2	K562	blood:
3	chr10:43624629..43626379-chr10:43749891..43752180,2	K562	blood:
4	chr10:43746418..43748826-chr10:43749692..43752083,4	K562	blood:
5	chr10:43749536..43751095-chr10:43809193..43811814,2	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1059484	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10793422	0.87[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10793424	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10793426	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10793427	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899778	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10899779	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899780	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10899781	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899782	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10899786	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11238476	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11238479	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11238481	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11238483	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11238485	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11238490	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11528481	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12220534	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12220560	0.90[EUR][1000 genomes]
rs12268309	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12356643	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12360493	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12416428	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1254958	0.87[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1254959	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1254960	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1254962	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1254963	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1254965	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1254967	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1254968	0.86[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1270015	0.87[ASN][1000 genomes]
rs1317214	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1879301	1.00[YRI][hapmap]
rs1879307	1.00[YRI][hapmap]
rs1879310	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1915142	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2003317	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2075912	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2115817	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2257767	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2293020	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2435337	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2435338	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2435339	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2435354	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2435376	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2435377	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2435383	0.81[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2435384	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2435385	0.90[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs2460551	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2460556	0.82[JPT][hapmap]
rs2460557	0.84[JPT][hapmap]
rs2503848	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2503849	0.87[ASN][1000 genomes]
rs2503853	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2503860	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2503863	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2503864	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2503881	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505506	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2505511	0.82[ASN][1000 genomes]
rs2505553	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505557	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2565200	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2742237	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs2742240	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs3004214	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4648313	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60845448	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61268333	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61845684	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7073849	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7093409	0.83[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7096500	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7098236	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7098237	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs871763	0.84[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv895086	chr10:43731521-43767816	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1044422	chr10:43731521-43860307	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	esv1846074	chr10:43744741-43761629	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10899787	CSGALNACT2	cis	Thyroid	GTEx
rs10899787	CSGALNACT2	cis	Heart Left Ventricle	GTEx
rs10899787	CSGALNACT2	cis	Nerve Tibial	GTEx
rs10899787	CSGALNACT2	cis	Artery Tibial	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43743800-43755000	Weak transcription	Brain Angular Gyrus	brain
2	chr10:43744600-43751800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr10:43744600-43756200	Enhancers	Spleen	Spleen
4	chr10:43745000-43751800	Enhancers	Primary T cells fromperipheralblood	blood
5	chr10:43746000-43750800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr10:43746200-43760000	Weak transcription	A549	lung
7	chr10:43746600-43751000	Weak transcription	Brain Anterior Caudate	brain
8	chr10:43747200-43750800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr10:43747200-43751200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr10:43747200-43751200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:43747400-43751200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr10:43747400-43751200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr10:43747400-43752000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr10:43747600-43751200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:43748600-43751200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:43749000-43750200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr10:43749000-43757200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr10:43749200-43750600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr10:43749400-43751600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr10:43749600-43750400	Weak transcription	Placenta	Placenta
21	chr10:43749600-43751400	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr10:43749800-43750200	Flanking Bivalent TSS/Enh	HepG2	liver
23	chr10:43749800-43751200	Enhancers	Lung	lung
24	chr10:43749800-43752400	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr10:43750000-43752200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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