Variant report

Variant	rs6602259
Chromosome Location	chr10:5844628-5844629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:5795617..5797655-chr10:5843237..5845319,2	K562	blood:
2	chr10:5844325..5846252-chr10:5848114..5849873,2	K562	blood:
3	chr10:5831602..5838072-chr10:5842540..5850784,8	MCF-7	breast:
4	chr10:5833873..5836597-chr10:5841720..5845063,3	K562	blood:
5	chr10:5832056..5836941-chr10:5839805..5845063,7	K562	blood:
6	chr10:5841031..5843716-chr10:5843918..5845552,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10508296	0.89[ASN][1000 genomes]
rs10737013	0.83[EUR][1000 genomes]
rs10737019	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10737021	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10752069	0.83[EUR][1000 genomes]
rs10752110	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10752111	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10795347	1.00[CHB][hapmap]
rs10795515	0.82[EUR][1000 genomes]
rs10795520	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10795541	0.89[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10795547	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10905065	0.83[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10905137	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10905234	0.90[ASN][1000 genomes]
rs10905255	0.87[ASN][1000 genomes]
rs10905256	0.83[ASN][1000 genomes]
rs11255085	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11255228	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1317420	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1533215	0.87[ASN][1000 genomes]
rs1567706	0.84[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1567707	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs1858447	0.84[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs1967487	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2175630	0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs2244755	0.81[TSI][hapmap]
rs2246399	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2380199	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2380202	0.81[EUR][1000 genomes]
rs2380203	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2497	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2797488	0.84[TSI][hapmap]
rs2890365	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2892078	0.84[EUR][1000 genomes]
rs3736462	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4748913	0.81[EUR][1000 genomes]
rs4748916	0.80[EUR][1000 genomes]
rs60840965	0.81[EUR][1000 genomes]
rs6602240	0.84[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs6602278	0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7071811	0.87[EUR][1000 genomes]
rs7078711	0.84[TSI][hapmap]
rs7089100	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs7096742	0.84[TSI][hapmap]
rs7100576	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7896749	0.82[EUR][1000 genomes]
rs7909733	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7913067	0.89[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7916827	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9423726	0.82[TSI][hapmap]
rs9423936	0.81[CHB][hapmap];0.84[CHD][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6602259	GDI2	Cis_1M	lymphoblastoid	RTeQTL
rs6602259	GDI2	cis	cerebellum	SCAN
rs6602259	GDI2	cis	uninvolved skin	skin_eQTL
rs6602259	GDI2	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5768000-5849400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:5797400-5847400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr10:5818000-5854200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:5827800-5848800	Weak transcription	Stomach Mucosa	stomach
5	chr10:5827800-5851200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr10:5828800-5847000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:5832000-5848000	Weak transcription	Fetal Heart	heart
8	chr10:5834600-5853600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr10:5834800-5845200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr10:5837800-5847000	Weak transcription	Psoas Muscle	Psoas
11	chr10:5837800-5854200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr10:5838000-5851400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr10:5838600-5845200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr10:5838600-5851200	Weak transcription	Brain Angular Gyrus	brain
15	chr10:5838600-5851400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr10:5838800-5847400	Weak transcription	Hela-S3	cervix
17	chr10:5838800-5848800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr10:5838800-5849400	Weak transcription	Brain Substantia Nigra	brain
19	chr10:5838800-5851600	Weak transcription	Fetal Brain Male	brain
20	chr10:5840600-5851800	Weak transcription	Colonic Mucosa	Colon
21	chr10:5840800-5846200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr10:5840800-5851600	Weak transcription	Fetal Kidney	kidney
23	chr10:5841400-5851400	Weak transcription	Aorta	Aorta
24	chr10:5841400-5851800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr10:5841400-5853400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr10:5841600-5848800	Weak transcription	Right Ventricle	heart
27	chr10:5841600-5848800	Weak transcription	Spleen	Spleen
28	chr10:5841600-5849600	Weak transcription	Lung	lung
29	chr10:5841600-5851400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr10:5841600-5853400	Weak transcription	Esophagus	oesophagus
31	chr10:5841800-5846400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr10:5841800-5847600	Weak transcription	Left Ventricle	heart
33	chr10:5841800-5851200	Weak transcription	Brain Germinal Matrix	brain
34	chr10:5842000-5851200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr10:5842200-5845000	Weak transcription	HepG2	liver
36	chr10:5842400-5847000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr10:5842400-5847400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr10:5842400-5847400	Weak transcription	Colon Smooth Muscle	Colon
39	chr10:5842400-5851400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr10:5842600-5845000	Weak transcription	Primary B cells from peripheral blood	blood
41	chr10:5842600-5845000	Weak transcription	Ovary	ovary
42	chr10:5842600-5845200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr10:5842600-5845200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr10:5842600-5846200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr10:5842600-5846400	Weak transcription	Adipose Nuclei	Adipose
46	chr10:5842600-5846400	Weak transcription	Fetal Thymus	thymus
47	chr10:5842600-5846600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr10:5842600-5847000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr10:5842600-5847200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr10:5842600-5847200	Weak transcription	Placenta	Placenta

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