Variant report

Variant	rs1942
Chromosome Location	chr15:41774423-41774424
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41768891..41771490-chr15:41773165..41774729,2	K562	blood:
2	chr15:41773035..41782898-chr15:41783132..41789747,15	K562	blood:
3	chr15:41768098..41770012-chr15:41773199..41776033,2	K562	blood:

Variant related genes	Relation type
ENSG00000137815	Chromatin interaction
ENSG00000137825	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11070327	1.00[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap]
rs12440045	0.81[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1655558	0.86[EUR][1000 genomes]
rs4924544	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7169278	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7173571	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8032846	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1942	STARD9	cis	cerebellum	SCAN
rs1942	NDUFAF1	cis	Muscle Skeletal	GTEx
rs1942	NUSAP1	cis	cerebellum	SCAN
rs1942	NDUFAF1	cis	parietal	SCAN
rs1942	RTF1	cis	Thyroid	GTEx
rs1942	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs1942	RPAP1	cis	parietal	SCAN
rs1942	NDUFAF1	cis	lymphoblastoid	seeQTL
rs1942	NDUFAF1	cis	cerebellum	SCAN
rs1942	NDUFAF1	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41724200-41777200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:41745200-41775800	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:41753000-41775000	Strong transcription	Fetal Stomach	stomach
4	chr15:41753800-41776800	Strong transcription	Fetal Muscle Leg	muscle
5	chr15:41754200-41775200	Strong transcription	Primary T cells from cord blood	blood
6	chr15:41754200-41776000	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:41754400-41774600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:41754400-41775000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:41754400-41776800	Strong transcription	Placenta	Placenta
10	chr15:41755000-41775600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr15:41755400-41775200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:41756800-41776200	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:41757000-41776200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:41757000-41776400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:41757200-41774600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr15:41757200-41775400	Strong transcription	Fetal Thymus	thymus
17	chr15:41757400-41776800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr15:41759000-41775000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:41760800-41775600	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr15:41761000-41776400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr15:41762000-41776000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:41764600-41775800	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr15:41764800-41776000	Strong transcription	Fetal Lung	lung
24	chr15:41765000-41774800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr15:41765000-41774800	Strong transcription	Brain Cingulate Gyrus	brain
26	chr15:41765000-41777200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr15:41765200-41775400	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr15:41765400-41775400	Strong transcription	Adipose Nuclei	Adipose
29	chr15:41765600-41774800	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr15:41765600-41774800	Strong transcription	Dnd41	blood
31	chr15:41765600-41775000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:41765600-41775400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:41765600-41775600	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:41765600-41775600	Strong transcription	Brain Hippocampus Middle	brain
35	chr15:41765600-41775800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:41765600-41775800	Strong transcription	Brain Anterior Caudate	brain
37	chr15:41765600-41775800	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:41765600-41776000	Strong transcription	Brain Substantia Nigra	brain
39	chr15:41765600-41776800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:41765600-41778400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:41765800-41774600	Strong transcription	Brain Germinal Matrix	brain
42	chr15:41765800-41775400	Strong transcription	HSMMtube	muscle
43	chr15:41766600-41776000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:41766600-41776400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:41767600-41775400	Strong transcription	Liver	Liver
46	chr15:41767600-41776200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:41767600-41776600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:41768000-41774600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr15:41769400-41775600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr15:41769600-41775000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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