Variant report

Variant	rs12080601
Chromosome Location	chr1:47051874-47051875
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KNCN-3	chr1:47051546-47051941	NONHSAT003025

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11211305	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11211307	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211308	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11211310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211311	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211314	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211318	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211321	0.83[AFR][1000 genomes]
rs11211322	0.83[AFR][1000 genomes]
rs12074458	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12083666	0.83[AFR][1000 genomes]
rs12088719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12090191	0.83[AFR][1000 genomes]
rs12092171	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12093618	0.83[AFR][1000 genomes]
rs12095096	1.00[EUR][1000 genomes]
rs12096548	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3766235	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs41305866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56089465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61783115	1.00[EUR][1000 genomes]
rs61783117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61783120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61783122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61783123	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61783125	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS 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
4	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS 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	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS 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	nsv1009899	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv534954	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active 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	12 gene(s)	inside rSNPs	diseases
9	nsv1011892	chr1:47010519-47067492	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47021000-47057000	Weak transcription	Fetal Brain Male	brain
2	chr1:47021800-47054600	Weak transcription	A549	lung
3	chr1:47022400-47053600	Strong transcription	Thymus	Thymus
4	chr1:47023200-47060000	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:47023800-47053200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:47024000-47054800	Weak transcription	HUVEC	blood vessel
7	chr1:47025600-47062400	Weak transcription	Fetal Heart	heart
8	chr1:47035200-47053000	Strong transcription	Spleen	Spleen
9	chr1:47035600-47053400	Strong transcription	Fetal Muscle Trunk	muscle
10	chr1:47036000-47056400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:47036000-47060000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr1:47036400-47053200	Strong transcription	Fetal Stomach	stomach
13	chr1:47037800-47057000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:47038400-47053200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:47039000-47052600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:47039000-47054800	Weak transcription	Hela-S3	cervix
17	chr1:47039200-47053000	Weak transcription	Right Atrium	heart
18	chr1:47039200-47060400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:47039600-47052400	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:47039600-47060000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:47040000-47053000	Strong transcription	Left Ventricle	heart
22	chr1:47040000-47053200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:47040200-47060400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:47040800-47053000	Strong transcription	NHEK	skin
25	chr1:47041000-47053600	Strong transcription	Aorta	Aorta
26	chr1:47041200-47052400	Strong transcription	Right Ventricle	heart
27	chr1:47041200-47053200	Strong transcription	Fetal Intestine Small	intestine
28	chr1:47041200-47054800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:47041600-47053200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:47042200-47057200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:47042400-47052800	Strong transcription	Colon Smooth Muscle	Colon
32	chr1:47042400-47057200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:47042600-47060400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr1:47042600-47069000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:47042800-47052400	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:47042800-47054600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:47042800-47056600	Weak transcription	Small Intestine	intestine
38	chr1:47042800-47068800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:47043600-47053600	Strong transcription	HMEC	breast
40	chr1:47045600-47068800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:47046200-47056400	Weak transcription	NH-A	brain
42	chr1:47046200-47069000	Weak transcription	Fetal Kidney	kidney
43	chr1:47046400-47055200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:47046400-47057200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:47046600-47054800	Weak transcription	Stomach Mucosa	stomach
46	chr1:47046800-47053000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:47046800-47053200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:47046800-47054800	Weak transcription	HSMM	muscle
49	chr1:47047200-47053600	Strong transcription	Lung	lung
50	chr1:47047400-47052000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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