Variant report

Variant	rs10491420
Chromosome Location	chr5:37070395-37070396
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:37068907..37070430-chr5:37371231..37374108,2	K562	blood:

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

Variant related genes	Relation type
ENSG00000113569	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs56762878	1.00[AMR][1000 genomes]
rs59505293	1.00[AMR][1000 genomes]
rs60219552	1.00[AMR][1000 genomes]
rs61739227	1.00[AMR][1000 genomes]
rs73750913	1.00[AMR][1000 genomes]
rs73750921	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73750931	1.00[AMR][1000 genomes]
rs73750941	1.00[AMR][1000 genomes]
rs73750947	1.00[AMR][1000 genomes]
rs73750949	1.00[AMR][1000 genomes]
rs73750951	1.00[AMR][1000 genomes]
rs7706007	1.00[AMR][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10491420	ABP1	trans	lymphoblastoid	seeQTL
rs10491420	STAG3	trans	lymphoblastoid	seeQTL

Chromatin state (count:93 , 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	chr5:37053400-37072000	Weak transcription	NHLF	lung
4	chr5:37054600-37071200	Weak transcription	Brain Angular Gyrus	brain
5	chr5:37055800-37071000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:37058600-37090000	Weak transcription	Right Ventricle	heart
7	chr5:37059600-37071000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:37060600-37079800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:37061000-37076800	Weak transcription	A549	lung
10	chr5:37061200-37096800	Weak transcription	Psoas Muscle	Psoas
11	chr5:37061200-37103400	Weak transcription	Fetal Kidney	kidney
12	chr5:37061800-37079600	Weak transcription	Aorta	Aorta
13	chr5:37064200-37073000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:37064200-37105000	Weak transcription	Fetal Brain Male	brain
15	chr5:37064600-37104000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr5:37064800-37070600	Weak transcription	NHDF-Ad	bronchial
17	chr5:37064800-37071600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:37064800-37072400	Weak transcription	HepG2	liver
19	chr5:37064800-37086800	Weak transcription	Pancreas	Pancrea
20	chr5:37064800-37087000	Weak transcription	Colonic Mucosa	Colon
21	chr5:37064800-37093600	Weak transcription	Brain Germinal Matrix	brain
22	chr5:37065000-37071400	Weak transcription	Brain Substantia Nigra	brain
23	chr5:37065000-37071600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:37065000-37071600	Weak transcription	HMEC	breast
25	chr5:37065000-37072200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:37065000-37078200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:37065000-37079600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:37065000-37079600	Weak transcription	HSMMtube	muscle
29	chr5:37065000-37083000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:37065000-37083000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:37065000-37084400	Weak transcription	Fetal Intestine Small	intestine
32	chr5:37065000-37086800	Weak transcription	Lung	lung
33	chr5:37065000-37087000	Weak transcription	Esophagus	oesophagus
34	chr5:37065000-37092600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr5:37065000-37092600	Weak transcription	Small Intestine	intestine
36	chr5:37065000-37097400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:37065000-37099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:37065000-37107600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:37065200-37071400	Weak transcription	HUVEC	blood vessel
40	chr5:37065200-37071600	Weak transcription	Brain Anterior Caudate	brain
41	chr5:37065200-37071600	Weak transcription	NH-A	brain
42	chr5:37065200-37072000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:37065200-37077000	Weak transcription	Fetal Muscle Leg	muscle
44	chr5:37065200-37078600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr5:37065200-37079600	Weak transcription	Left Ventricle	heart
46	chr5:37065200-37080400	Weak transcription	Fetal Stomach	stomach
47	chr5:37065200-37090800	Weak transcription	Primary T cells from cord blood	blood
48	chr5:37065200-37103400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr5:37065400-37071200	Weak transcription	Brain Hippocampus Middle	brain
50	chr5:37065400-37077000	Weak transcription	Thymus	Thymus

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