Variant report

Variant	rs3087852
Chromosome Location	chr17:38137364-38137365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38136765..38137554-chr2:110371108..110371776,2	Hela-S3	cervix:
2	chr17:38136187..38139299-chr17:38140015..38144342,5	K562	blood:
3	chr14:76126953..76127942-chr17:38136732..38137532,2	Hela-S3	cervix:
4	chr17:38136818..38137469-chr7:142960335..142961013,2	HCT-116	colon:
5	chr17:38136379..38138502-chr17:38148012..38149919,2	K562	blood:
6	chr17:38137253..38140627-chr17:38150200..38152697,4	MCF-7	breast:
7	chr17:38073305..38078163-chr17:38135913..38140017,5	K562	blood:
8	chr17:38117802..38119525-chr17:38136512..38138841,3	K562	blood:
9	chr1:1284400..1285140-chr17:38136711..38137477,2	Hela-S3	cervix:
10	chr17:38094255..38096841-chr17:38137196..38138815,2	MCF-7	breast:
11	chr17:38136308..38139120-chr17:38254735..38257246,2	MCF-7	breast:
12	chr17:38073305..38078633-chr17:38135671..38140017,6	K562	blood:
13	chr17:38137113..38139548-chr17:38217878..38220392,2	K562	blood:
14	chr17:38063855..38068073-chr17:38135195..38137481,3	K562	blood:
15	chr17:38135295..38137617-chr17:38176453..38178456,2	K562	blood:
16	chr17:37703880..37705005-chr17:38136510..38137377,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000126368	Chromatin interaction
ENSG00000108344	Chromatin interaction
ENSG00000167258	Chromatin interaction
ENSG00000119685	Chromatin interaction
ENSG00000172057	Chromatin interaction
ENSG00000186522	Chromatin interaction
ENSG00000107404	Chromatin interaction
ENSG00000197448	Chromatin interaction
ENSG00000167914	Chromatin interaction
ENSG00000133935	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000126351	Chromatin interaction
ENSG00000073605	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11078930	0.96[ASN][1000 genomes]
rs11078931	0.94[ASN][1000 genomes]
rs11078935	0.81[ASN][1000 genomes]
rs11078936	0.81[ASN][1000 genomes]
rs11654208	0.81[ASN][1000 genomes]
rs11655264	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655655	0.81[ASN][1000 genomes]
rs11658328	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11867302	0.93[ASN][1000 genomes]
rs12309	0.87[ASN][1000 genomes]
rs12450688	0.81[ASN][1000 genomes]
rs12450800	0.95[ASN][1000 genomes]
rs12451547	0.89[ASN][1000 genomes]
rs12451897	0.89[ASN][1000 genomes]
rs12453334	0.96[ASN][1000 genomes]
rs12453341	0.89[ASN][1000 genomes]
rs12453343	0.89[ASN][1000 genomes]
rs12453764	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12602514	0.85[ASN][1000 genomes]
rs12939682	0.81[ASN][1000 genomes]
rs12940405	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2227319	0.89[ASN][1000 genomes]
rs2227321	0.89[ASN][1000 genomes]
rs2227333	0.89[ASN][1000 genomes]
rs2241244	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2241245	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2270401	0.89[ASN][1000 genomes]
rs2302774	0.89[ASN][1000 genomes]
rs2302777	0.89[ASN][1000 genomes]
rs2305481	0.98[ASN][1000 genomes]
rs2305482	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs25645	0.88[ASN][1000 genomes]
rs34003767	0.81[ASN][1000 genomes]
rs34342173	0.90[ASN][1000 genomes]
rs34453912	0.87[ASN][1000 genomes]
rs34648856	0.96[ASN][1000 genomes]
rs34933056	0.90[ASN][1000 genomes]
rs35272691	0.91[ASN][1000 genomes]
rs36071767	0.84[ASN][1000 genomes]
rs3744245	0.96[ASN][1000 genomes]
rs3785550	0.94[ASN][1000 genomes]
rs3816472	0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3859187	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3859189	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935281	0.83[ASN][1000 genomes]
rs4065321	0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4072639	0.83[ASN][1000 genomes]
rs4433838	0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7502971	0.85[ASN][1000 genomes]
rs8066582	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs8070444	0.98[ASN][1000 genomes]
rs8071037	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs8073254	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs8075668	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898547	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9915252	0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9916158	0.88[ASN][1000 genomes]

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	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3087852	MED24	cis	Nerve Tibial	GTEx
rs3087852	GSDMA	cis	Esophagus Muscularis	GTEx
rs3087852	GSDMA	cis	Nerve Tibial	GTEx
rs3087852	GSDMA	cis	Adipose Subcutaneous	GTEx
rs3087852	MED24	cis	Artery Tibial	GTEx
rs3087852	GSDMA	cis	lung	GTEx
rs3087852	GSDMA	cis	Thyroid	GTEx
rs3087852	GSDMA	cis	Artery Aorta	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38135400-38137800	Active TSS	Duodenum Mucosa	Duodenum
2	chr17:38136000-38137600	Active TSS	Brain Germinal Matrix	brain
3	chr17:38136000-38137600	Active TSS	Rectal Smooth Muscle	rectum
4	chr17:38136000-38138600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr17:38136200-38137600	Active TSS	Fetal Brain Male	brain
6	chr17:38136200-38137800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:38136200-38138000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr17:38136200-38138000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr17:38136200-38138000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:38136200-38138000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:38136200-38138000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr17:38136200-38138000	Active TSS	Fetal Brain Female	brain
13	chr17:38136200-38138000	Active TSS	Fetal Kidney	kidney
14	chr17:38136200-38138200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr17:38136200-38138200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr17:38136200-38138200	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr17:38136200-38138200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr17:38136200-38138200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr17:38136200-38138200	Active TSS	Right Atrium	heart
20	chr17:38136200-38138400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr17:38136200-38138400	Active TSS	Esophagus	oesophagus
22	chr17:38136200-38138400	Active TSS	Left Ventricle	heart
23	chr17:38136200-38138600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr17:38136200-38138600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr17:38136200-38138600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:38136200-38138600	Active TSS	Colonic Mucosa	Colon
27	chr17:38136200-38138600	Active TSS	Ovary	ovary
28	chr17:38136200-38138600	Active TSS	Right Ventricle	heart
29	chr17:38136200-38139000	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr17:38136400-38137400	Active TSS	Primary B cells from peripheral blood	blood
31	chr17:38136400-38137400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr17:38136400-38137400	Active TSS	Stomach Smooth Muscle	stomach
33	chr17:38136400-38137600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr17:38136400-38137600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr17:38136400-38137600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr17:38136400-38137600	Active TSS	Brain Substantia Nigra	brain
37	chr17:38136400-38137600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr17:38136400-38137600	Active TSS	Fetal Muscle Leg	muscle
39	chr17:38136400-38137800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr17:38136400-38137800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr17:38136400-38137800	Active TSS	Brain Cingulate Gyrus	brain
42	chr17:38136400-38137800	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr17:38136400-38137800	Active TSS	Fetal Lung	lung
44	chr17:38136400-38137800	Active TSS	Fetal Stomach	stomach
45	chr17:38136400-38137800	Active TSS	Fetal Thymus	thymus
46	chr17:38136400-38137800	Active TSS	Thymus	Thymus
47	chr17:38136400-38138000	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr17:38136400-38138000	Active TSS	Colon Smooth Muscle	Colon
49	chr17:38136400-38138000	Active TSS	Placenta Amnion	Placenta Amnion
50	chr17:38136400-38138000	Bivalent/Poised TSS	HepG2	liver

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