Variant report

Variant	rs17143628
Chromosome Location	chr10:5832205-5832206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:5831897-5832240	HepG2	liver:	n/a	n/a
2	POLR2A	chr10:5832108-5832319	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:5831602..5838072-chr10:5842540..5850784,8	MCF-7	breast:
2	chr10:5830218..5833166-chr10:5848485..5851225,2	K562	blood:
3	chr10:5832056..5836941-chr10:5839805..5845063,7	K562	blood:
4	chr10:5831817..5834005-chr10:5852525..5854271,2	K562	blood:

Variant related genes	Relation type
GDI2	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11596435	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11920	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1858446	0.85[EUR][1000 genomes]
rs2890364	0.84[EUR][1000 genomes]
rs2892078	0.80[AFR][1000 genomes]
rs7071811	0.81[AFR][1000 genomes]
rs7095103	0.83[EUR][1000 genomes]
rs72772355	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72772358	0.86[AMR][1000 genomes];0.88[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17143628	GDI2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5762600-5843400	Strong transcription	Dnd41	blood
2	chr10:5762800-5843000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:5768000-5849400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:5797400-5847400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr10:5798000-5842800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:5798200-5843000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr10:5798600-5842800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr10:5805000-5843200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:5818000-5854200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:5818400-5842800	Strong transcription	Duodenum Mucosa	Duodenum
11	chr10:5818800-5842600	Strong transcription	Fetal Thymus	thymus
12	chr10:5819600-5844000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr10:5820200-5833400	Strong transcription	HepG2	liver
14	chr10:5820200-5840400	Strong transcription	HSMM	muscle
15	chr10:5820200-5842800	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr10:5820400-5843000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr10:5820400-5843000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr10:5820600-5842800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:5821800-5838800	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr10:5822000-5843800	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr10:5822200-5842600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr10:5822200-5843400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr10:5822400-5833400	Strong transcription	K562	blood
24	chr10:5822400-5842600	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr10:5822400-5842800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr10:5822600-5842800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr10:5822600-5842800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr10:5823600-5842600	Strong transcription	Placenta	Placenta
29	chr10:5823800-5833400	Strong transcription	Left Ventricle	heart
30	chr10:5823800-5842600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr10:5823800-5842600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr10:5823800-5843400	Strong transcription	Thymus	Thymus
33	chr10:5824000-5842600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:5824000-5842600	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr10:5824000-5843400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:5824200-5833400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
37	chr10:5824200-5842800	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr10:5824200-5843400	Strong transcription	Fetal Intestine Large	intestine
39	chr10:5824600-5833600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr10:5824600-5842800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr10:5824600-5843400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr10:5824800-5833400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr10:5825000-5842800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr10:5825400-5836200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr10:5825800-5833200	Strong transcription	Fetal Lung	lung
46	chr10:5826000-5833000	Strong transcription	NHEK	skin
47	chr10:5826200-5833400	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr10:5826200-5839000	Strong transcription	HMEC	breast
49	chr10:5826400-5832600	Strong transcription	Spleen	Spleen
50	chr10:5826400-5834000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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