Variant report

Variant	rs7916827
Chromosome Location	chr10:5850468-5850469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5830218..5833166-chr10:5848485..5851225,2	K562	blood:
2	chr10:5850191..5852972-chr10:5915096..5916950,2	K562	blood:
3	chr10:5831602..5838072-chr10:5842540..5850784,8	MCF-7	breast:
4	chr10:5830187..5831718-chr10:5849725..5851751,2	K562	blood:
5	chr10:5849264..5850852-chr10:5930459..5932960,2	MCF-7	breast:
6	chr10:5839916..5843685-chr10:5848628..5853676,5	K562	blood:

Variant related genes	Relation type
ENSG00000134452	Chromatin interaction
ENSG00000134461	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10508296	0.85[ASN][1000 genomes]
rs10737013	0.80[EUR][1000 genomes]
rs10737019	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10737021	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10752069	0.80[EUR][1000 genomes]
rs10752110	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10752111	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10795520	0.81[EUR][1000 genomes]
rs10795541	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10795547	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10905065	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10905137	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10905234	0.86[ASN][1000 genomes]
rs10905255	0.85[ASN][1000 genomes]
rs10905256	0.81[ASN][1000 genomes]
rs11255085	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11255228	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1317420	0.81[EUR][1000 genomes]
rs1533215	0.85[ASN][1000 genomes]
rs1567706	0.83[EUR][1000 genomes]
rs1567707	0.83[EUR][1000 genomes]
rs1858447	0.85[EUR][1000 genomes]
rs1967487	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2246399	0.81[ASN][1000 genomes]
rs2380203	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2497	0.82[EUR][1000 genomes]
rs2890365	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2892078	0.83[EUR][1000 genomes]
rs3736462	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6602240	0.81[EUR][1000 genomes]
rs6602259	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6602278	0.84[ASN][1000 genomes]
rs7071811	0.86[EUR][1000 genomes]
rs7089100	0.86[EUR][1000 genomes]
rs7100576	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7896749	0.82[EUR][1000 genomes]
rs7909733	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7913067	0.83[AMR][1000 genomes];0.81[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
rs7916827	GDI2	Cis_1M	lymphoblastoid	RTeQTL

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	chr10:5827800-5851200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr10:5834600-5853600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr10:5837800-5854200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:5838000-5851400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr10:5838600-5851200	Weak transcription	Brain Angular Gyrus	brain
7	chr10:5838600-5851400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr10:5838800-5851600	Weak transcription	Fetal Brain Male	brain
9	chr10:5840600-5851800	Weak transcription	Colonic Mucosa	Colon
10	chr10:5840800-5851600	Weak transcription	Fetal Kidney	kidney
11	chr10:5841400-5851400	Weak transcription	Aorta	Aorta
12	chr10:5841400-5851800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr10:5841400-5853400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr10:5841600-5851400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr10:5841600-5853400	Weak transcription	Esophagus	oesophagus
16	chr10:5841800-5851200	Weak transcription	Brain Germinal Matrix	brain
17	chr10:5842000-5851200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr10:5842400-5851400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr10:5842600-5851400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr10:5842600-5851600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:5842600-5853200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr10:5842600-5853200	Weak transcription	HSMMtube	muscle
23	chr10:5842800-5850800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr10:5842800-5851600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr10:5843200-5851400	Weak transcription	NHLF	lung
26	chr10:5843400-5851600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr10:5843600-5854400	Weak transcription	Gastric	stomach
28	chr10:5845000-5851800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr10:5845200-5851200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr10:5846600-5851000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr10:5846600-5852000	Genic enhancers	Primary B cells from peripheral blood	blood
32	chr10:5846800-5851400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr10:5847200-5851200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr10:5847600-5854600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr10:5847800-5851000	Weak transcription	Thymus	Thymus
36	chr10:5847800-5851400	Weak transcription	Osteobl	bone
37	chr10:5848000-5851200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr10:5848000-5851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr10:5848000-5851800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:5848000-5852400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr10:5848200-5850600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr10:5848200-5851200	Weak transcription	Hela-S3	cervix
43	chr10:5848200-5851200	Weak transcription	HMEC	breast
44	chr10:5848200-5851400	Weak transcription	NH-A	brain
45	chr10:5848400-5852200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr10:5848400-5852200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr10:5848800-5850600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr10:5848800-5850600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr10:5848800-5854200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr10:5849000-5851200	Weak transcription	Primary hematopoietic stem cells	blood

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