Variant report

Variant	rs1858446
Chromosome Location	chr10:5852172-5852173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr10:5851475-5852175	HepG2	liver:	n/a	n/a
2	NFATC1	chr10:5851374-5852764	GM12878	blood:	n/a	n/a
3	POLR2A	chr10:5851288-5853864	HepG2	liver:	n/a	n/a
4	MXI1	chr10:5851510-5852580	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:5850191..5852972-chr10:5915096..5916950,2	K562	blood:
2	chr10:5851448..5853265-chr10:5875008..5877610,2	MCF-7	breast:
3	chr10:5711853..5714027-chr10:5850909..5854727,3	K562	blood:
4	chr10:5487246..5491032-chr10:5851403..5854778,3	K562	blood:
5	chr10:5487246..5489927-chr10:5851403..5853447,2	K562	blood:
6	chr10:5810933..5813093-chr10:5852041..5854972,2	K562	blood:
7	chr10:5851570..5858995-chr10:5881654..5887342,9	K562	blood:
8	chr10:5850869..5856128-chr10:5879241..5885807,8	K562	blood:
9	chr10:5839916..5843685-chr10:5848628..5853676,5	K562	blood:
10	chr10:5851291..5853357-chr10:5931908..5934075,2	K562	blood:
11	chr10:5850597..5853484-chr10:5898526..5901196,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272764	TF binding region
ENSG00000057608	Chromatin interaction
ENSG00000173848	Chromatin interaction
ENSG00000134452	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1046393	1.00[CHD][hapmap];0.82[MKK][hapmap];0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1129614	0.94[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.85[YRI][hapmap]
rs11596435	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11920	0.83[TSI][hapmap]
rs17143628	0.85[EUR][1000 genomes]
rs2890364	0.97[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3793707	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs45575338	0.86[ASN][1000 genomes]
rs4748572	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]
rs4749379	0.94[CHB][hapmap];0.85[YRI][hapmap]
rs55837307	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs55910451	0.80[AFR][1000 genomes]
rs58859669	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59007376	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7095103	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72772354	0.87[ASN][1000 genomes]
rs72772355	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72772358	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72772376	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72772390	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72772400	0.92[ASN][1000 genomes]
rs72774070	0.84[ASN][1000 genomes]
rs72774075	0.87[ASN][1000 genomes]
rs72774077	0.87[ASN][1000 genomes]
rs72774078	0.87[ASN][1000 genomes]
rs74116316	0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
5	nsv831775	chr10:5804335-6000849	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv515935	chr10:5820394-5869839	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv549896	chr10:5820394-5880066	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1858446	GDI2	cis	Artery Tibial	GTEx
rs1858446	GDI2	cis	cerebellum	SCAN
rs1858446	GDI2	cis	parietal	SCAN
rs1858446	GDI2	Cis_1M	lymphoblastoid	RTeQTL
rs1858446	GDI2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5818000-5854200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:5834600-5853600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:5837800-5854200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:5841400-5853400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:5841600-5853400	Weak transcription	Esophagus	oesophagus
6	chr10:5842600-5853200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr10:5842600-5853200	Weak transcription	HSMMtube	muscle
8	chr10:5843600-5854400	Weak transcription	Gastric	stomach
9	chr10:5847600-5854600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:5848000-5852400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr10:5848400-5852200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr10:5848400-5852200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr10:5848800-5854200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr10:5849800-5852400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr10:5850200-5853200	Weak transcription	Fetal Thymus	thymus
16	chr10:5850200-5853400	Weak transcription	Placenta	Placenta
17	chr10:5850200-5853400	Weak transcription	Lung	lung
18	chr10:5850200-5853400	Weak transcription	Pancreas	Pancrea
19	chr10:5850200-5854600	Weak transcription	Spleen	Spleen
20	chr10:5850600-5853200	Weak transcription	Left Ventricle	heart
21	chr10:5850600-5853400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr10:5850600-5853400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr10:5850600-5853400	Weak transcription	Fetal Stomach	stomach
24	chr10:5851000-5852800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr10:5851000-5853000	Enhancers	Fetal Heart	heart
26	chr10:5851000-5853200	Enhancers	Adipose Nuclei	Adipose
27	chr10:5851200-5852200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr10:5851200-5852200	Enhancers	Hela-S3	cervix
29	chr10:5851200-5852400	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr10:5851200-5852400	Enhancers	Stomach Mucosa	stomach
31	chr10:5851200-5852400	Enhancers	HSMM	muscle
32	chr10:5851200-5852600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr10:5851200-5852600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr10:5851200-5852600	Enhancers	Fetal Muscle Leg	muscle
35	chr10:5851200-5852800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:5851200-5852800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr10:5851200-5853000	Enhancers	Brain Germinal Matrix	brain
38	chr10:5851200-5853000	Flanking Active TSS	GM12878-XiMat	blood
39	chr10:5851200-5853200	Enhancers	Brain Angular Gyrus	brain
40	chr10:5851200-5853200	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr10:5851200-5853400	Enhancers	Colon Smooth Muscle	Colon
42	chr10:5851200-5853600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr10:5851200-5853800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr10:5851200-5854000	Enhancers	Placenta Amnion	Placenta Amnion
45	chr10:5851200-5854800	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr10:5851200-5854800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:5851400-5852200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
48	chr10:5851400-5852200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr10:5851400-5852200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr10:5851400-5852200	Flanking Active TSS	HepG2	liver

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