Variant report

Variant	rs72888238
Chromosome Location	chr2:47713257-47713258
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNK12-1	chr2:47713153-47714936	ENSG00000236558.2

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs17036586	1.00[AMR][1000 genomes]
rs17036616	1.00[AMR][1000 genomes]
rs17036622	0.86[AFR][1000 genomes]
rs17039236	1.00[AMR][1000 genomes]
rs17217849	1.00[AMR][1000 genomes]
rs17217961	1.00[AMR][1000 genomes]
rs17218648	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17224122	1.00[AMR][1000 genomes]
rs17224724	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17224738	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17224815	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1800151	1.00[AMR][1000 genomes]
rs55815447	1.00[AMR][1000 genomes]
rs55905016	1.00[AMR][1000 genomes]
rs56076616	1.00[AMR][1000 genomes]
rs56958162	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56983268	1.00[AMR][1000 genomes]
rs57972954	1.00[AMR][1000 genomes]
rs58012164	1.00[AMR][1000 genomes]
rs58080795	1.00[AMR][1000 genomes]
rs58930161	1.00[AMR][1000 genomes]
rs59974084	1.00[AMR][1000 genomes]
rs60121180	1.00[AMR][1000 genomes]
rs60512750	1.00[AMR][1000 genomes]
rs61282650	1.00[AMR][1000 genomes]
rs61635665	1.00[AMR][1000 genomes]
rs72882725	1.00[AMR][1000 genomes]
rs72882752	1.00[AMR][1000 genomes]
rs72882765	1.00[AMR][1000 genomes]
rs72882783	1.00[AMR][1000 genomes]
rs72882786	1.00[AMR][1000 genomes]
rs72882796	1.00[AMR][1000 genomes]
rs72882802	1.00[AMR][1000 genomes]
rs72884625	1.00[AMR][1000 genomes]
rs72884632	1.00[AMR][1000 genomes]
rs72884676	1.00[AMR][1000 genomes]
rs72886304	1.00[AMR][1000 genomes]
rs72886358	1.00[AMR][1000 genomes]
rs72888237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72888263	1.00[AMR][1000 genomes]
rs73927801	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73927802	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47631400-47714400	Weak transcription	Right Ventricle	heart
2	chr2:47633000-47714000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:47658000-47714200	Weak transcription	Small Intestine	intestine
4	chr2:47658200-47713400	Weak transcription	Fetal Heart	heart
5	chr2:47658200-47714200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:47658200-47714800	Weak transcription	HSMMtube	muscle
7	chr2:47658200-47724800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:47658400-47713600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:47658400-47716000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:47685000-47715000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:47691000-47714000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:47691600-47714200	Weak transcription	Ovary	ovary
13	chr2:47691600-47714400	Weak transcription	Spleen	Spleen
14	chr2:47691600-47715400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:47691600-47715600	Weak transcription	NHEK	skin
16	chr2:47691600-47716000	Weak transcription	Gastric	stomach
17	chr2:47691600-47716000	Weak transcription	Pancreas	Pancrea
18	chr2:47692000-47714400	Weak transcription	Placenta	Placenta
19	chr2:47692800-47713400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:47693200-47713600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:47693600-47715400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:47693600-47716800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:47694200-47715600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:47696000-47716000	Weak transcription	NHLF	lung
25	chr2:47696800-47716000	Weak transcription	Lung	lung
26	chr2:47697000-47714400	Weak transcription	Esophagus	oesophagus
27	chr2:47697000-47716200	Weak transcription	Fetal Brain Female	brain
28	chr2:47697200-47715400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr2:47697600-47715600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:47699000-47714200	Weak transcription	Brain Anterior Caudate	brain
31	chr2:47699200-47713400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:47699200-47714200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr2:47700400-47714800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:47700600-47714400	Weak transcription	Brain Germinal Matrix	brain
35	chr2:47702400-47714200	Weak transcription	Aorta	Aorta
36	chr2:47702800-47727000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:47703800-47716000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:47703800-47722000	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:47704000-47714000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr2:47704200-47713600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:47704200-47716200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:47704400-47714400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:47704400-47714400	Weak transcription	Stomach Mucosa	stomach
44	chr2:47705800-47717000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:47706000-47715800	Weak transcription	HUVEC	blood vessel
46	chr2:47706000-47715800	Weak transcription	NH-A	brain
47	chr2:47706200-47716200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:47706600-47716200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr2:47708400-47716000	Weak transcription	HSMM	muscle
50	chr2:47710000-47716200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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