Variant report

Variant	rs10752069
Chromosome Location	chr10:5752403-5752404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5748194..5752835-chr10:5754048..5756817,4	MCF-7	breast:
2	chr10:5751112..5753798-chr10:5754382..5757716,3	K562	blood:
3	chr10:5733787..5736575-chr10:5751182..5753712,2	MCF-7	breast:
4	chr10:5749331..5751583-chr10:5752146..5753784,2	MCF-7	breast:
5	chr10:5733731..5736743-chr10:5750015..5755601,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108021	Chromatin interaction
ENSG00000226647	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10737012	0.88[EUR][1000 genomes]
rs10737013	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10737019	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10737021	0.81[EUR][1000 genomes]
rs10752110	0.90[EUR][1000 genomes]
rs10752111	0.85[EUR][1000 genomes]
rs10795347	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10795485	0.91[EUR][1000 genomes]
rs10795488	0.89[EUR][1000 genomes]
rs10795510	0.88[EUR][1000 genomes]
rs10795515	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10795520	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10795541	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10795547	0.81[EUR][1000 genomes]
rs10905065	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10905137	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11255085	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11255228	0.88[EUR][1000 genomes]
rs12571639	0.89[EUR][1000 genomes]
rs1317420	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1967487	0.80[EUR][1000 genomes]
rs2244755	0.91[EUR][1000 genomes]
rs2246399	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2380199	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2380203	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2386623	0.90[ASN][1000 genomes]
rs2386624	0.90[ASN][1000 genomes]
rs2497	0.82[EUR][1000 genomes]
rs2797488	0.86[EUR][1000 genomes]
rs2890365	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2892078	0.81[EUR][1000 genomes]
rs3736462	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6602259	0.83[EUR][1000 genomes]
rs7078711	0.88[EUR][1000 genomes]
rs7096742	0.88[EUR][1000 genomes]
rs7100576	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7909733	0.81[EUR][1000 genomes]
rs7909988	0.88[EUR][1000 genomes]
rs7913067	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7916827	0.80[EUR][1000 genomes]
rs9423726	0.88[EUR][1000 genomes]
rs9423930	0.87[EUR][1000 genomes]
rs9423936	0.92[ASN][1000 genomes]
rs9423948	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9424221	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv1796213	chr10:5716555-5766165	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv522415	chr10:5721653-5768493	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv1050663	chr10:5737979-5785918	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv528504	chr10:5739054-5754611	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10752069	GDI2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5734800-5763400	Weak transcription	HSMM	muscle
2	chr10:5735200-5767000	Weak transcription	Fetal Muscle Leg	muscle
3	chr10:5735400-5761600	Weak transcription	NHEK	skin
4	chr10:5735400-5762000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:5735800-5752800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr10:5736400-5753000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:5738600-5752800	Weak transcription	Right Atrium	heart
8	chr10:5738600-5769000	Weak transcription	Left Ventricle	heart
9	chr10:5739600-5752800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr10:5740200-5752800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr10:5740400-5768600	Weak transcription	Psoas Muscle	Psoas
12	chr10:5741400-5760600	Weak transcription	Small Intestine	intestine
13	chr10:5741400-5765600	Weak transcription	A549	lung
14	chr10:5741600-5753400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr10:5743200-5753600	Weak transcription	HepG2	liver
16	chr10:5743200-5762600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr10:5744200-5753000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr10:5746800-5752800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr10:5749000-5752800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr10:5749000-5753200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr10:5749400-5752800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr10:5749600-5753400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr10:5749600-5753600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr10:5749800-5752600	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr10:5749800-5753400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr10:5750000-5763400	Weak transcription	K562	blood
27	chr10:5750200-5752600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr10:5751400-5752800	Enhancers	Primary T cells from cord blood	blood
29	chr10:5751600-5753200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:5751600-5763800	Weak transcription	Osteobl	bone
31	chr10:5751800-5752600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr10:5751800-5752600	Enhancers	Fetal Lung	lung
33	chr10:5751800-5752800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr10:5751800-5753000	Enhancers	Dnd41	blood
35	chr10:5751800-5753200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr10:5751800-5753800	Enhancers	Brain Hippocampus Middle	brain
37	chr10:5751800-5753800	Flanking Active TSS	GM12878-XiMat	blood
38	chr10:5752000-5752600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr10:5752000-5752600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr10:5752000-5753200	Enhancers	Liver	Liver
41	chr10:5752200-5752600	Enhancers	Duodenum Mucosa	Duodenum
42	chr10:5752200-5753200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr10:5752200-5753200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr10:5752200-5753400	Weak transcription	Colon Smooth Muscle	Colon
45	chr10:5752200-5753800	Enhancers	NHLF	lung
46	chr10:5752200-5763600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr10:5752400-5752600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr10:5752400-5752600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr10:5752400-5752600	Enhancers	Brain Substantia Nigra	brain
50	chr10:5752400-5752600	Enhancers	Rectal Smooth Muscle	rectum

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