Variant report

Variant	rs300055
Chromosome Location	chr5:37072824-37072825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:37068070..37069786-chr5:37070605..37073109,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NIPBL-3	chr5:37069673-37075373	NONHSAT101047

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs13176880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs150380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes]
rs151944	0.87[EUR][1000 genomes]
rs158622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs158623	0.89[EUR][1000 genomes]
rs158624	0.83[EUR][1000 genomes]
rs158791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs158796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes]
rs158803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs159749	0.92[EUR][1000 genomes]
rs159751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs159753	0.95[EUR][1000 genomes]
rs159755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs159913	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs168662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs184182	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs186173	0.91[EUR][1000 genomes]
rs188541	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs292182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs292183	0.91[EUR][1000 genomes]
rs292184	0.90[EUR][1000 genomes]
rs292194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.94[EUR][1000 genomes]
rs292195	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs296962	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.91[EUR][1000 genomes]
rs300046	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs300049	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs300051	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs300053	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs300058	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs300060	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs300061	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs300063	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs300064	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs300065	0.93[EUR][1000 genomes]
rs301859	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs301901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs301917	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3104057	0.90[EUR][1000 genomes]
rs388098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6875748	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][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:87 , 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	chr5:37058600-37090000	Weak transcription	Right Ventricle	heart
3	chr5:37060600-37079800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:37061000-37076800	Weak transcription	A549	lung
5	chr5:37061200-37096800	Weak transcription	Psoas Muscle	Psoas
6	chr5:37061200-37103400	Weak transcription	Fetal Kidney	kidney
7	chr5:37061800-37079600	Weak transcription	Aorta	Aorta
8	chr5:37064200-37073000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:37064200-37105000	Weak transcription	Fetal Brain Male	brain
10	chr5:37064600-37104000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr5:37064800-37086800	Weak transcription	Pancreas	Pancrea
12	chr5:37064800-37087000	Weak transcription	Colonic Mucosa	Colon
13	chr5:37064800-37093600	Weak transcription	Brain Germinal Matrix	brain
14	chr5:37065000-37078200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:37065000-37079600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:37065000-37079600	Weak transcription	HSMMtube	muscle
17	chr5:37065000-37083000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:37065000-37083000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:37065000-37084400	Weak transcription	Fetal Intestine Small	intestine
20	chr5:37065000-37086800	Weak transcription	Lung	lung
21	chr5:37065000-37087000	Weak transcription	Esophagus	oesophagus
22	chr5:37065000-37092600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr5:37065000-37092600	Weak transcription	Small Intestine	intestine
24	chr5:37065000-37097400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr5:37065000-37099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:37065000-37107600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:37065200-37077000	Weak transcription	Fetal Muscle Leg	muscle
28	chr5:37065200-37078600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr5:37065200-37079600	Weak transcription	Left Ventricle	heart
30	chr5:37065200-37080400	Weak transcription	Fetal Stomach	stomach
31	chr5:37065200-37090800	Weak transcription	Primary T cells from cord blood	blood
32	chr5:37065200-37103400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:37065400-37077000	Weak transcription	Thymus	Thymus
34	chr5:37065400-37079400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr5:37065400-37080200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:37065600-37078200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr5:37065600-37078200	Weak transcription	Dnd41	blood
38	chr5:37065600-37079200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:37065600-37085000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr5:37065600-37086600	Weak transcription	Fetal Intestine Large	intestine
41	chr5:37065600-37089400	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr5:37065600-37102400	Weak transcription	Placenta	Placenta
43	chr5:37065800-37087000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr5:37066000-37077000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:37066000-37078200	Weak transcription	Fetal Brain Female	brain
46	chr5:37066000-37079600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:37066000-37086400	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr5:37066200-37078200	Weak transcription	Adipose Nuclei	Adipose
49	chr5:37066200-37085800	Weak transcription	Primary B cells from cord blood	blood
50	chr5:37066400-37078200	Weak transcription	Liver	Liver

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