Variant report

Variant	rs12195877
Chromosome Location	chr6:2398948-2398949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:12)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WRNIP1-2	chr6:2398811-2398981	ENSG00000250903
2	lnc-WRNIP1-2	chr6:2398811-2399000	ENSG00000250903
3	lnc-WRNIP1-2	chr6:2398811-2399012	ENSG00000250903
4	lnc-WRNIP1-2	chr6:2398809-2399012	ENSG00000250903
5	lnc-WRNIP1-2	chr6:2398811-2399012	XLOC_005127
6	lnc-WRNIP1-2	chr6:2398823-2399012	XLOC_005127
7	lnc-WRNIP1-2	chr6:2398806-2399012	XLOC_005127
8	lnc-WRNIP1-2	chr6:2398811-2399012	XLOC_005127
9	lnc-WRNIP1-2	chr6:2398811-2399012	NONHSAT106620
10	lnc-WRNIP1-2	chr6:2398811-2399012	NONHSAT106659
11	lnc-WRNIP1-2	chr6:2398891-2399012	ENSG00000250903.4
12	lnc-WRNIP1-2	chr6:2398811-2399012	ENSG00000250903.4

No data

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10458063	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10458138	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10458139	0.80[EUR][1000 genomes]
rs10458140	0.80[EUR][1000 genomes]
rs10458141	0.80[EUR][1000 genomes]
rs10458142	0.80[EUR][1000 genomes]
rs11242760	0.88[EUR][1000 genomes]
rs11242761	0.88[EUR][1000 genomes]
rs11242766	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11242769	0.83[EUR][1000 genomes]
rs11753825	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11758482	0.80[EUR][1000 genomes]
rs12189681	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12189724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196223	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12199363	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12199637	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12205452	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12206851	0.80[EUR][1000 genomes]
rs12209220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12209322	0.83[AMR][1000 genomes]
rs12209326	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12209801	0.90[EUR][1000 genomes]
rs12210286	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12210452	0.83[EUR][1000 genomes]
rs12213643	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12525444	0.85[AFR][1000 genomes]
rs12525582	0.88[EUR][1000 genomes]
rs12526475	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12527624	0.89[EUR][1000 genomes]
rs12528202	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12662045	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13196348	0.85[AFR][1000 genomes]
rs13214014	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13214565	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13220392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2073003	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2076470	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2294659	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34885387	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35144026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612673	0.88[EUR][1000 genomes]
rs3734506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3817904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71552116	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71552117	0.88[EUR][1000 genomes]
rs764345	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9328099	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9503155	0.82[EUR][1000 genomes]
rs983027	0.83[EUR][1000 genomes]
rs983028	0.80[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	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases
10	esv2763527	chr6:2390712-2400244	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2390600-2399000	Weak transcription	Fetal Intestine Large	intestine
2	chr6:2391600-2399400	Weak transcription	Primary T cells from cord blood	blood
3	chr6:2392400-2400600	Weak transcription	Aorta	Aorta
4	chr6:2392400-2414400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:2395400-2403800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:2396800-2400800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:2396800-2415400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:2397000-2399600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:2397000-2402800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:2397000-2409400	Weak transcription	HepG2	liver
11	chr6:2397200-2410200	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:2397400-2399400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:2397400-2402400	Weak transcription	Psoas Muscle	Psoas
14	chr6:2397400-2403000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:2397400-2404200	Weak transcription	Fetal Kidney	kidney
16	chr6:2397600-2399400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:2397600-2399600	Strong transcription	Fetal Intestine Small	intestine
18	chr6:2397600-2399800	Strong transcription	Pancreas	Pancrea
19	chr6:2397800-2400000	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:2397800-2400400	Weak transcription	Fetal Brain Female	brain
21	chr6:2397800-2406800	Weak transcription	Fetal Heart	heart
22	chr6:2398000-2399400	Weak transcription	Fetal Lung	lung
23	chr6:2398000-2399600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:2398000-2399800	Strong transcription	Fetal Stomach	stomach
25	chr6:2398000-2400400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:2398000-2400800	Weak transcription	Adipose Nuclei	Adipose
27	chr6:2398000-2401000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:2398000-2401200	Weak transcription	Colonic Mucosa	Colon
29	chr6:2398000-2403200	Weak transcription	Brain Substantia Nigra	brain
30	chr6:2398000-2412600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:2398200-2399600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:2398200-2399600	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:2398200-2400600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:2398200-2400800	Strong transcription	Liver	Liver
35	chr6:2398200-2401000	Strong transcription	Ovary	ovary
36	chr6:2398200-2405400	Weak transcription	Right Ventricle	heart
37	chr6:2398400-2401800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr6:2398600-2399200	ZNF genes & repeats	Lung	lung
39	chr6:2398600-2403800	Weak transcription	Gastric	stomach
40	chr6:2398600-2405400	Weak transcription	Spleen	Spleen
41	chr6:2398800-2399800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr6:2398800-2402200	Strong transcription	Left Ventricle	heart

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