Variant report

Variant	rs1129614
Chromosome Location	chr10:5808086-5808087
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5726952..5729225-chr10:5806393..5808626,2	MCF-7	breast:
2	chr10:5488493..5490077-chr10:5808073..5811424,3	MCF-7	breast:
3	chr10:5805727..5811403-chr10:5852267..5856532,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000057608	Chromatin interaction
ENSG00000173848	Chromatin interaction
ENSG00000272764	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1046393	0.95[CHD][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11920	1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs1858446	0.94[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.85[YRI][hapmap]
rs2275774	0.87[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs2797496	0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs2890364	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3793707	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45575338	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4748572	1.00[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4749379	0.88[CHB][hapmap];1.00[YRI][hapmap]
rs4750553	0.89[ASW][hapmap]
rs55837307	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55910451	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56033057	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56251728	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58859669	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59007376	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7095103	0.81[ASN][1000 genomes]
rs72772354	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72772355	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72772358	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72772376	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72772390	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72772400	0.82[EUR][1000 genomes]
rs72774070	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72774075	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72774077	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72774078	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74116316	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1129614	GDI2	Cis_1M	lymphoblastoid	RTeQTL
rs1129614	GDI2	cis	cerebellum	SCAN
rs1129614	GDI2	cis	Whole Blood	GTEx
rs1129614	GDI2	cis	parietal	SCAN

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	chr10:5781400-5818600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:5783400-5816600	Strong transcription	Primary B cells from peripheral blood	blood
6	chr10:5784800-5818000	Weak transcription	Stomach Mucosa	stomach
7	chr10:5786200-5816400	Weak transcription	Right Atrium	heart
8	chr10:5788000-5818000	Strong transcription	Duodenum Mucosa	Duodenum
9	chr10:5795000-5817800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr10:5796000-5822400	Strong transcription	Fetal Intestine Large	intestine
11	chr10:5797200-5819000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr10:5797400-5816600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr10:5797400-5816800	Strong transcription	Fetal Thymus	thymus
14	chr10:5797400-5847400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr10:5797600-5811800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
16	chr10:5797600-5812200	Strong transcription	Primary hematopoietic stem cells	blood
17	chr10:5797600-5812200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr10:5797600-5812400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr10:5797600-5814600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr10:5797600-5816200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr10:5797600-5817200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr10:5797600-5817800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr10:5797600-5817800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr10:5797800-5811200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr10:5797800-5812000	Strong transcription	Primary T cells from cord blood	blood
26	chr10:5797800-5816400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr10:5798000-5812600	Strong transcription	HMEC	breast
28	chr10:5798000-5817000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr10:5798000-5817600	Strong transcription	Primary B cells from cord blood	blood
30	chr10:5798000-5818200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr10:5798000-5842800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr10:5798200-5815400	Strong transcription	NH-A	brain
33	chr10:5798200-5817000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr10:5798200-5843000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr10:5798400-5816600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr10:5798400-5817800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr10:5798400-5817800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr10:5798600-5810400	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr10:5798600-5811400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr10:5798600-5811600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr10:5798600-5812200	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr10:5798600-5812200	Strong transcription	HSMM	muscle
43	chr10:5798600-5812200	Strong transcription	K562	blood
44	chr10:5798600-5815200	Strong transcription	Adipose Nuclei	Adipose
45	chr10:5798600-5817000	Strong transcription	Placenta	Placenta
46	chr10:5798600-5817400	Strong transcription	Osteobl	bone
47	chr10:5798600-5817800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr10:5798600-5818400	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr10:5798600-5820200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr10:5798600-5842800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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