Variant report

Variant	rs13395751
Chromosome Location	chr2:54238794-54238795
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACYP2-6	chr2:54234735-54240630	NONHSAT070717

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10188834	0.83[AMR][1000 genomes]
rs10190353	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199995	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1049894	0.88[AMR][1000 genomes]
rs11125517	0.83[AMR][1000 genomes]
rs11884857	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11886024	0.82[EUR][1000 genomes]
rs11886366	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887593	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11889527	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890472	0.87[EUR][1000 genomes]
rs11891000	0.87[EUR][1000 genomes]
rs11904365	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13389673	0.82[EUR][1000 genomes]
rs13401491	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13401719	0.83[AMR][1000 genomes]
rs13402778	0.81[EUR][1000 genomes]
rs13417051	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13432387	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2112120	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2161083	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28571698	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28699646	0.88[AMR][1000 genomes]
rs3930909	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs41536750	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58920915	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60769690	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60776154	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6545382	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6715161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719990	1.00[AMR][1000 genomes]
rs6723722	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6730494	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731217	0.82[EUR][1000 genomes]
rs6731911	0.82[EUR][1000 genomes]
rs6745729	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6748686	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6751340	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6756424	0.81[EUR][1000 genomes]
rs6761648	0.87[EUR][1000 genomes]
rs72904915	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72906704	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906711	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72906714	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7556936	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7559651	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7560575	0.82[EUR][1000 genomes]
rs7583508	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7588134	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7588319	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7599335	0.82[EUR][1000 genomes]
rs7608085	0.88[AMR][1000 genomes]
rs9309251	0.82[EUR][1000 genomes]
rs9678301	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54208400-54248200	Weak transcription	Lung	lung
2	chr2:54211400-54243000	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:54213600-54249800	Weak transcription	Left Ventricle	heart
4	chr2:54215000-54242800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:54216400-54242000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:54217000-54248200	Weak transcription	Gastric	stomach
7	chr2:54217200-54239600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:54224400-54239600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:54226000-54240000	Weak transcription	Primary B cells from cord blood	blood
10	chr2:54226200-54239600	Weak transcription	Adipose Nuclei	Adipose
11	chr2:54226600-54243000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:54226800-54239000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:54226800-54239200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr2:54228400-54239600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:54228800-54243400	Weak transcription	Fetal Lung	lung
16	chr2:54229000-54243000	Weak transcription	Right Atrium	heart
17	chr2:54229200-54245800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:54234400-54242800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:54235400-54242800	Weak transcription	Ovary	ovary
20	chr2:54235400-54246400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:54235800-54243600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:54237200-54239600	Weak transcription	Brain Substantia Nigra	brain
23	chr2:54237200-54239800	Weak transcription	Brain Anterior Caudate	brain
24	chr2:54237200-54243000	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:54237200-54243000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:54237400-54243000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:54238000-54239000	Weak transcription	Primary T cells from cord blood	blood
28	chr2:54238000-54242400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr2:54238200-54239600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr2:54238200-54239600	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:54238200-54239600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:54238200-54246800	Weak transcription	Spleen	Spleen
33	chr2:54238400-54242600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:54238600-54242600	Weak transcription	NHDF-Ad	bronchial

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