Variant report

Variant	rs309948
Chromosome Location	chr5:42953224-42953225
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF131-4	chr5:42950963-42959174	XLOC_004362

Extended variants
information (count: 125 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10036916	0.97[ASN][1000 genomes]
rs10064003	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10522	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10941598	0.83[ASN][1000 genomes]
rs10941604	0.82[ASN][1000 genomes]
rs10941605	0.82[ASN][1000 genomes]
rs11743123	0.82[ASN][1000 genomes]
rs11747435	0.82[ASN][1000 genomes]
rs11747714	0.97[ASN][1000 genomes]
rs11958008	0.82[ASN][1000 genomes]
rs12697439	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13169690	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13179934	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs160709	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs17300176	0.81[ASN][1000 genomes]
rs186323	0.94[ASN][1000 genomes]
rs186324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188693	0.82[ASN][1000 genomes]
rs1902101	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2100473	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2124069	0.84[AMR][1000 genomes]
rs222060	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2247280	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2253450	0.82[ASN][1000 genomes]
rs2329994	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2329995	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2432097	0.83[ASN][1000 genomes]
rs2548334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548336	0.98[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2548339	0.94[ASN][1000 genomes]
rs2548341	0.91[ASN][1000 genomes]
rs2548343	0.92[ASN][1000 genomes]
rs2548345	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548346	0.90[ASN][1000 genomes]
rs2548349	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2548350	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2548353	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2548356	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2548373	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2548374	0.82[ASN][1000 genomes]
rs2548382	0.84[ASN][1000 genomes]
rs2603620	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2603625	0.82[ASN][1000 genomes]
rs2603626	0.81[ASN][1000 genomes]
rs2603627	0.82[ASN][1000 genomes]
rs2603628	0.81[ASN][1000 genomes]
rs2603629	0.81[ASN][1000 genomes]
rs2603630	0.82[ASN][1000 genomes]
rs2603631	0.82[ASN][1000 genomes]
rs2603632	0.82[ASN][1000 genomes]
rs2603633	0.82[ASN][1000 genomes]
rs2603634	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2603644	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2603649	0.83[ASN][1000 genomes]
rs2603650	0.83[ASN][1000 genomes]
rs2603651	0.82[ASN][1000 genomes]
rs2603656	0.82[ASN][1000 genomes]
rs2876993	0.87[ASN][1000 genomes]
rs2882295	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2924817	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs309909	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs309911	0.81[ASN][1000 genomes]
rs309912	0.83[ASN][1000 genomes]
rs309914	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs309921	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs309922	0.91[ASN][1000 genomes]
rs309923	0.94[ASN][1000 genomes]
rs309924	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs309925	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs309926	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs309927	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs309938	0.82[ASN][1000 genomes]
rs309939	0.81[ASN][1000 genomes]
rs309940	0.81[ASN][1000 genomes]
rs309950	0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs316395	0.85[AMR][1000 genomes]
rs316414	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs316416	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs316419	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs316422	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs3849696	0.82[ASN][1000 genomes]
rs3849697	0.97[ASN][1000 genomes]
rs3893725	0.87[ASN][1000 genomes]
rs3909456	0.94[ASN][1000 genomes]
rs4033115	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4092293	0.89[AMR][1000 genomes]
rs4092294	0.90[AMR][1000 genomes]
rs4296812	0.87[AMR][1000 genomes]
rs613825	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs643307	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6451660	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6451661	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6451662	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6861491	0.83[ASN][1000 genomes]
rs6875214	0.90[AMR][1000 genomes]
rs6880163	0.96[ASN][1000 genomes]
rs6882794	0.90[ASN][1000 genomes]
rs6883097	0.95[ASN][1000 genomes]
rs6889150	0.82[ASN][1000 genomes]
rs6889271	0.83[ASN][1000 genomes]
rs6890457	0.81[ASN][1000 genomes]
rs6890469	0.82[ASN][1000 genomes]
rs6895732	0.82[ASN][1000 genomes]
rs6899257	0.97[ASN][1000 genomes]
rs768441	0.89[AMR][1000 genomes]
rs7707797	0.84[ASN][1000 genomes]
rs7715065	0.81[ASN][1000 genomes]
rs7733383	0.97[ASN][1000 genomes]
rs9292862	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv968909	chr5:42903982-42953465	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	esv1806082	chr5:42906572-42967215	Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv1813779	chr5:42906572-42992040	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	esv3346992	chr5:42921680-42970055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
12	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
13	nsv1020910	chr5:42929799-43000021	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
14	nsv537738	chr5:42929799-43000021	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
15	nsv528880	chr5:42940230-42967215	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv515883	chr5:42949688-42967215	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42949000-42953600	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr5:42950600-42953600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:42950600-42954200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:42950600-42954600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:42950800-42953400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr5:42951000-42953600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:42951600-42954800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:42952000-42953400	Enhancers	Spleen	Spleen
9	chr5:42952000-42953600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
10	chr5:42952400-42954200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:42952600-42953400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:42952800-42953400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
13	chr5:42952800-42953400	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr5:42952800-42953400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr5:42952800-42953400	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr5:42952800-42953400	Enhancers	Right Ventricle	heart
17	chr5:42952800-42953400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
18	chr5:42952800-42953600	Enhancers	Primary B cells from peripheral blood	blood
19	chr5:42952800-42953600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
20	chr5:42952800-42953600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr5:42953000-42953400	ZNF genes & repeats	Right Atrium	heart
22	chr5:42953000-42953400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
23	chr5:42953000-42953600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:42953000-42954200	ZNF genes & repeats	Thymus	Thymus
25	chr5:42953000-42954400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
26	chr5:42953000-42954400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:42953000-42954400	ZNF genes & repeats	NHDF-Ad	bronchial
28	chr5:42953000-42954600	ZNF genes & repeats	NHLF	lung
29	chr5:42953000-42954800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:42953200-42953400	Bivalent Enhancer	Primary B cells from cord blood	blood
31	chr5:42953200-42953400	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr5:42953200-42953400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr5:42953200-42953400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:42953200-42953400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr5:42953200-42953400	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
36	chr5:42953200-42953400	Bivalent Enhancer	Brain Hippocampus Middle	brain
37	chr5:42953200-42953400	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:42953200-42953400	Bivalent Enhancer	Brain Substantia Nigra	brain
39	chr5:42953200-42953400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
40	chr5:42953200-42953400	Bivalent Enhancer	Esophagus	oesophagus
41	chr5:42953200-42953400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
42	chr5:42953200-42953400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
43	chr5:42953200-42953600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
44	chr5:42953200-42953600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr5:42953200-42953600	Bivalent Enhancer	Small Intestine	intestine
46	chr5:42953200-42953800	Enhancers	Primary T cells fromperipheralblood	blood
47	chr5:42953200-42953800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr5:42953200-42954000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
49	chr5:42953200-42954000	Flanking Active TSS	HUVEC	blood vessel
50	chr5:42953200-42954000	ZNF genes & repeats	NH-A	brain

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