Variant report

Variant	rs16903490
Chromosome Location	chr5:37068046-37068047
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NIPBL-3	chr5:37067383-37069132	NONHSAT101047

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10512664	0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs12654646	0.82[ASN][1000 genomes]
rs12658479	0.92[GIH][hapmap];1.00[LWK][hapmap]
rs13166829	0.82[AFR][1000 genomes]
rs13171061	0.82[AFR][1000 genomes]
rs13177573	0.82[AFR][1000 genomes]
rs13177875	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13181187	0.82[AFR][1000 genomes]
rs13183090	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13184464	0.85[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs13188136	0.82[AFR][1000 genomes]
rs151946	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs158792	0.81[EUR][1000 genomes]
rs158793	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs158794	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs158802	0.81[ASN][1000 genomes]
rs159140	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs159141	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs167146	0.83[EUR][1000 genomes]
rs16903459	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16903531	0.90[GIH][hapmap];1.00[LWK][hapmap];0.82[YRI][hapmap]
rs245588	0.82[ASN][1000 genomes]
rs292160	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs292179	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs292180	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs292181	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs292186	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs292196	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs293748	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs293774	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs294695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34066351	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs34479946	0.92[ASN][1000 genomes]
rs34525350	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35011787	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35701604	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs468022	0.85[ASN][1000 genomes]
rs56261529	0.86[ASN][1000 genomes]
rs59398009	0.82[AFR][1000 genomes]
rs61748200	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6861906	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9632396	1.00[YRI][hapmap]
rs9637791	0.82[AFR][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	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv530225	chr5:36886635-37331912	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1024051	chr5:36899712-37303001	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv537725	chr5:36899712-37303001	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv530226	chr5:36906377-37606367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv917880	chr5:36948778-37115342	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	esv1802391	chr5:36958598-37242600	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv597822	chr5:36997953-37147152	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv534064	chr5:37054962-37586210	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36949600-37086800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:37035400-37071600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:37051000-37069200	Weak transcription	Fetal Heart	heart
4	chr5:37053400-37072000	Weak transcription	NHLF	lung
5	chr5:37054600-37071200	Weak transcription	Brain Angular Gyrus	brain
6	chr5:37055400-37068800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:37055800-37071000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:37058600-37090000	Weak transcription	Right Ventricle	heart
9	chr5:37059600-37071000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:37060600-37079800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:37061000-37076800	Weak transcription	A549	lung
12	chr5:37061200-37096800	Weak transcription	Psoas Muscle	Psoas
13	chr5:37061200-37103400	Weak transcription	Fetal Kidney	kidney
14	chr5:37061800-37079600	Weak transcription	Aorta	Aorta
15	chr5:37064200-37073000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:37064200-37105000	Weak transcription	Fetal Brain Male	brain
17	chr5:37064600-37104000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:37064800-37070600	Weak transcription	NHDF-Ad	bronchial
19	chr5:37064800-37071600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:37064800-37072400	Weak transcription	HepG2	liver
21	chr5:37064800-37086800	Weak transcription	Pancreas	Pancrea
22	chr5:37064800-37087000	Weak transcription	Colonic Mucosa	Colon
23	chr5:37064800-37093600	Weak transcription	Brain Germinal Matrix	brain
24	chr5:37065000-37068200	Weak transcription	Ovary	ovary
25	chr5:37065000-37068400	Weak transcription	K562	blood
26	chr5:37065000-37069600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:37065000-37070200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:37065000-37071400	Weak transcription	Brain Substantia Nigra	brain
29	chr5:37065000-37071600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:37065000-37071600	Weak transcription	HMEC	breast
31	chr5:37065000-37072200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:37065000-37078200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:37065000-37079600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr5:37065000-37079600	Weak transcription	HSMMtube	muscle
35	chr5:37065000-37083000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr5:37065000-37083000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:37065000-37084400	Weak transcription	Fetal Intestine Small	intestine
38	chr5:37065000-37086800	Weak transcription	Lung	lung
39	chr5:37065000-37087000	Weak transcription	Esophagus	oesophagus
40	chr5:37065000-37092600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr5:37065000-37092600	Weak transcription	Small Intestine	intestine
42	chr5:37065000-37097400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr5:37065000-37099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:37065000-37107600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr5:37065200-37068400	Weak transcription	Spleen	Spleen
46	chr5:37065200-37068800	Weak transcription	GM12878-XiMat	blood
47	chr5:37065200-37071400	Weak transcription	HUVEC	blood vessel
48	chr5:37065200-37071600	Weak transcription	Brain Anterior Caudate	brain
49	chr5:37065200-37071600	Weak transcription	NH-A	brain
50	chr5:37065200-37072000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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