Variant report

Variant	rs2173464
Chromosome Location	chr10:42454325-42454326
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10430806	0.88[AMR][1000 genomes]
rs10797137	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10908953	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10908961	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10908962	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908963	0.92[AMR][1000 genomes]
rs10908964	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908965	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908966	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908967	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10908979	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10908980	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10908982	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10909022	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1119185	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1119186	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1119187	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11265969	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11265983	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11265993	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11265994	0.84[AMR][1000 genomes]
rs11266039	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs11266159	0.87[ASN][1000 genomes]
rs11266165	0.84[ASN][1000 genomes]
rs11528793	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12775714	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1589587	0.84[AMR][1000 genomes]
rs1589588	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1603831	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1608190	0.86[AMR][1000 genomes]
rs1608194	0.84[ASN][1000 genomes]
rs1608197	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1608200	0.81[ASN][1000 genomes]
rs1818808	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1846408	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1851485	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1851486	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1851487	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1851490	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2201903	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2334905	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2335056	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2335068	0.86[ASN][1000 genomes]
rs34628100	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9663767	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9663778	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9664345	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9664628	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9664985	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9664992	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9665296	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9665476	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9665548	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9702416	0.95[CHB][hapmap];0.87[YRI][hapmap]
rs9702537	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9732766	0.81[AMR][1000 genomes]
rs9794047	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9794197	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9794218	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9794761	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550596	chr10:42362711-42467126	ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv3381019	chr10:42379843-42797311	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv3327265	chr10:42383108-42800080	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3381544	chr10:42385160-42597916	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv550608	chr10:42388730-42534628	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Enhancers	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3353947	chr10:42396093-42662055	ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3508721	chr10:42396414-42599602	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3508722	chr10:42396414-42599602	Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3527791	chr10:42396830-42596972	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3527792	chr10:42396830-42596972	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv3410118	chr10:42399439-42817641	ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	esv3149	chr10:42399672-42532552	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv550609	chr10:42401249-42478452	ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Enhancers	lncRNA	n/a	inside rSNPs	diseases
14	nsv550610	chr10:42401249-42503182	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription	lncRNA	n/a	inside rSNPs	diseases
15	esv4174	chr10:42408625-42539037	Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1044862	chr10:42433540-42523461	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS	lncRNA	n/a	inside rSNPs	diseases
17	nsv1041666	chr10:42433540-42525112	Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS	lncRNA	n/a	inside rSNPs	diseases
18	nsv1035511	chr10:42433540-42636467	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1050409	chr10:42433540-42690550	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv1041974	chr10:42433540-42760904	Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
21	nsv1052577	chr10:42433540-42827991	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
22	nsv1036341	chr10:42433540-42853111	ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv1036366	chr10:42433540-42853690	ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
24	esv2757380	chr10:42433540-42929116	ZNF genes & repeats Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
25	esv2759745	chr10:42433540-42929116	Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2173464	LINC00839	cis	lung	GTEx
rs2173464	RP11-313J2.1	cis	Nerve Tibial	GTEx
rs2173464	LINC00839	cis	Artery Aorta	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:42448000-42458200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr10:42453200-42454600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
3	chr10:42454000-42456600	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr10:42454000-42457000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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