Variant report

Variant	rs60840965
Chromosome Location	chr10:5823707-5823708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5822221..5824197-chr10:5834472..5837418,2	MCF-7	breast:
2	chr10:5822061..5824683-chr10:5847855..5850406,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10737012	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10737019	0.81[EUR][1000 genomes]
rs10737021	0.85[EUR][1000 genomes]
rs10752110	0.86[EUR][1000 genomes]
rs10752111	0.82[EUR][1000 genomes]
rs10795485	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10795488	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10795510	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10795541	0.88[EUR][1000 genomes]
rs10795547	0.84[EUR][1000 genomes]
rs10905137	0.86[EUR][1000 genomes]
rs11255085	0.84[EUR][1000 genomes]
rs11255228	0.85[EUR][1000 genomes]
rs11598374	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12571639	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1567706	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1567707	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1858447	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2175630	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2244755	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2380199	0.82[EUR][1000 genomes]
rs2380202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2380203	0.83[EUR][1000 genomes]
rs2497	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2797488	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2890365	0.80[EUR][1000 genomes]
rs2892078	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736462	0.86[EUR][1000 genomes]
rs4237365	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4748913	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4748916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6602240	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6602259	0.81[EUR][1000 genomes]
rs7071811	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7078711	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7089100	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7096742	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7100576	0.81[EUR][1000 genomes]
rs7896749	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7906719	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7909988	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7913067	0.82[EUR][1000 genomes]
rs9423726	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9423930	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv947730	chr10:5817688-5827238	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	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
8	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
rs60840965	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	chr10:5762600-5843400	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	chr10:5808400-5826400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:5808800-5825800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr10:5809000-5824400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr10:5810400-5824800	Weak transcription	Ovary	ovary
13	chr10:5811800-5824400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr10:5812000-5823800	Weak transcription	Fetal Kidney	kidney
15	chr10:5812000-5824000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:5817200-5831200	Weak transcription	Pancreas	Pancrea
17	chr10:5817800-5825000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr10:5817800-5826200	Weak transcription	HMEC	breast
19	chr10:5818000-5824600	Weak transcription	Colonic Mucosa	Colon
20	chr10:5818000-5824600	Weak transcription	Gastric	stomach
21	chr10:5818000-5826400	Weak transcription	Esophagus	oesophagus
22	chr10:5818000-5854200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr10:5818200-5824200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr10:5818200-5824200	Weak transcription	Fetal Brain Male	brain
25	chr10:5818200-5824800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr10:5818400-5823800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr10:5818400-5824000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr10:5818400-5824000	Weak transcription	Brain Anterior Caudate	brain
29	chr10:5818400-5824000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr10:5818400-5824200	Weak transcription	Fetal Brain Female	brain
31	chr10:5818400-5824600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr10:5818400-5826200	Weak transcription	Hela-S3	cervix
33	chr10:5818400-5826400	Weak transcription	Aorta	Aorta
34	chr10:5818400-5826400	Weak transcription	Spleen	Spleen
35	chr10:5818400-5842800	Strong transcription	Duodenum Mucosa	Duodenum
36	chr10:5818600-5824200	Weak transcription	NHEK	skin
37	chr10:5818800-5824000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr10:5818800-5824000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr10:5818800-5825400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr10:5818800-5825600	Weak transcription	Brain Angular Gyrus	brain
41	chr10:5818800-5826400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr10:5818800-5827400	Weak transcription	Stomach Mucosa	stomach
43	chr10:5818800-5842600	Strong transcription	Fetal Thymus	thymus
44	chr10:5819000-5824200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr10:5819000-5824200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr10:5819000-5824200	Weak transcription	Fetal Heart	heart
47	chr10:5819000-5825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr10:5819200-5824200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr10:5819200-5824400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr10:5819200-5824600	Weak transcription	Brain Cingulate Gyrus	brain

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