Variant report

Variant	rs11258943
Chromosome Location	chr10:6498723-6498724
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:6496886..6498996-chr10:6631205..6633815,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10906529	0.92[EUR][1000 genomes]
rs11258672	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11258708	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11258742	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11258747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11258856	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11259097	0.82[CHB][hapmap]
rs12220818	0.82[CHB][hapmap]
rs1537320	0.82[CHB][hapmap]
rs17155549	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17372283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34157770	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41301101	0.93[ASN][1000 genomes]
rs494800	0.82[CHB][hapmap]
rs584724	1.00[CHB][hapmap];0.86[TSI][hapmap]
rs602756	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61840390	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs648731	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs655732	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs667899	0.91[EUR][1000 genomes]
rs7082071	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72781716	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7910023	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7920162	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs806399	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv1047309	chr10:6495583-6714060	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11258943	GDI2	cis	lymphoblastoid	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6465800-6501400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr10:6477400-6503600	Weak transcription	Gastric	stomach
3	chr10:6480200-6501000	Weak transcription	Ovary	ovary
4	chr10:6481200-6500200	Weak transcription	Fetal Intestine Small	intestine
5	chr10:6488200-6499600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr10:6488200-6500200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr10:6488200-6502000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr10:6488400-6500200	Weak transcription	Esophagus	oesophagus
9	chr10:6488400-6506800	Weak transcription	K562	blood
10	chr10:6493400-6516200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr10:6493600-6501200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr10:6496000-6499000	Strong transcription	Fetal Thymus	thymus
13	chr10:6496000-6500200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr10:6496000-6502800	Strong transcription	Dnd41	blood
15	chr10:6496000-6508200	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr10:6496200-6498800	Strong transcription	Brain Substantia Nigra	brain
17	chr10:6496200-6499400	Strong transcription	Thymus	Thymus
18	chr10:6496200-6499600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
19	chr10:6496200-6500400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr10:6496200-6500600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr10:6496200-6500800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr10:6496200-6501000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr10:6496200-6501600	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr10:6496200-6501600	Strong transcription	Fetal Muscle Leg	muscle
25	chr10:6496200-6502000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:6496200-6502800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr10:6496200-6506200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr10:6496200-6508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr10:6496200-6509000	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr10:6496200-6511600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr10:6496200-6513000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr10:6496200-6514000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr10:6496200-6514200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr10:6496200-6514600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr10:6496400-6499000	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr10:6496400-6499200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr10:6496400-6499200	Strong transcription	Brain Angular Gyrus	brain
38	chr10:6496400-6502000	Strong transcription	Brain Hippocampus Middle	brain
39	chr10:6496600-6499000	Strong transcription	Pancreas	Pancrea
40	chr10:6496600-6506400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr10:6496600-6539200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr10:6496800-6503000	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr10:6497200-6500000	Weak transcription	Lung	lung
44	chr10:6497200-6500200	Weak transcription	Aorta	Aorta
45	chr10:6497400-6499200	Strong transcription	Brain Anterior Caudate	brain
46	chr10:6497400-6500200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr10:6497400-6501000	Weak transcription	NHEK	skin
48	chr10:6497600-6499000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr10:6497600-6501600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr10:6497600-6513200	Strong transcription	Primary T cells from cord blood	blood

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