Variant report

Variant	rs11594505
Chromosome Location	chr10:5820379-5820380
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	chr10:5819103..5820799-chr10:5833032..5835919,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1057943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10737018	0.81[MEX][hapmap]
rs11592993	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11593876	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11594846	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11595421	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11596702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11596832	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap]
rs11599810	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254067	0.81[MEX][hapmap]
rs2386620	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs2386664	0.83[EUR][1000 genomes]
rs2669135	0.81[MEX][hapmap]
rs2797484	0.81[EUR][1000 genomes]
rs2797487	0.81[MEX][hapmap]
rs2797491	0.81[MEX][hapmap]
rs2797501	1.00[MEX][hapmap];0.85[TSI][hapmap]
rs3736460	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs45549643	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56352451	0.84[EUR][1000 genomes]
rs59758327	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61832759	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61832860	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61832863	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61832864	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61832865	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61832866	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61832870	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61832872	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61832874	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61832878	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61836362	0.87[EUR][1000 genomes]
rs7076584	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7082754	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs7093027	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72772369	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72774084	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7475869	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7902987	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7907687	0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11594505	GDI2	cis	cerebellum	SCAN

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	chr10:5796000-5822400	Strong transcription	Fetal Intestine Large	intestine
5	chr10:5797400-5847400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr10:5798000-5842800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:5798200-5843000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr10:5798600-5842800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr10:5805000-5843200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr10:5807400-5821800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:5808400-5826400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:5808800-5825800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr10:5809000-5824400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr10:5810400-5824800	Weak transcription	Ovary	ovary
15	chr10:5811800-5824400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr10:5812000-5823800	Weak transcription	Fetal Kidney	kidney
17	chr10:5812000-5824000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:5812400-5821600	Weak transcription	Brain Germinal Matrix	brain
19	chr10:5814600-5822600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr10:5817200-5831200	Weak transcription	Pancreas	Pancrea
21	chr10:5817400-5821000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr10:5817800-5821800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr10:5817800-5825000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr10:5817800-5826200	Weak transcription	HMEC	breast
25	chr10:5818000-5824600	Weak transcription	Colonic Mucosa	Colon
26	chr10:5818000-5824600	Weak transcription	Gastric	stomach
27	chr10:5818000-5826400	Weak transcription	Esophagus	oesophagus
28	chr10:5818000-5854200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr10:5818200-5823600	Weak transcription	Placenta	Placenta
30	chr10:5818200-5824200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr10:5818200-5824200	Weak transcription	Fetal Brain Male	brain
32	chr10:5818200-5824800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr10:5818400-5820400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr10:5818400-5820400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr10:5818400-5821600	Weak transcription	Fetal Stomach	stomach
36	chr10:5818400-5821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr10:5818400-5821800	Weak transcription	Left Ventricle	heart
38	chr10:5818400-5821800	Weak transcription	Lung	lung
39	chr10:5818400-5822400	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr10:5818400-5823600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr10:5818400-5823800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr10:5818400-5824000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr10:5818400-5824000	Weak transcription	Brain Anterior Caudate	brain
44	chr10:5818400-5824000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr10:5818400-5824200	Weak transcription	Fetal Brain Female	brain
46	chr10:5818400-5824600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr10:5818400-5826200	Weak transcription	Hela-S3	cervix
48	chr10:5818400-5826400	Weak transcription	Aorta	Aorta
49	chr10:5818400-5826400	Weak transcription	Spleen	Spleen
50	chr10:5818400-5842800	Strong transcription	Duodenum Mucosa	Duodenum

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