Variant report

Variant	rs11259097
Chromosome Location	chr10:6521534-6521535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11258747	0.82[CHB][hapmap]
rs11258943	0.82[CHB][hapmap]
rs11259163	0.89[ASN][1000 genomes]
rs12220818	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs1537320	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17372283	0.82[CHB][hapmap]
rs494800	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs584724	0.82[CHB][hapmap]
rs6602745	0.85[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11259097	UCN3	cis	cerebellum	SCAN
rs11259097	PFKFB3	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6496600-6539200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr10:6498400-6537000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr10:6499000-6527800	Weak transcription	Pancreas	Pancrea
4	chr10:6499200-6562000	Weak transcription	Brain Anterior Caudate	brain
5	chr10:6501600-6527200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr10:6501800-6557000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr10:6503000-6533000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr10:6504600-6524200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr10:6509200-6541200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr10:6509800-6533000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:6510000-6572000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr10:6514000-6540000	Weak transcription	Psoas Muscle	Psoas
13	chr10:6516400-6535800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr10:6516600-6523000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr10:6517000-6531800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr10:6517200-6557800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:6517400-6523400	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr10:6517400-6524200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:6517400-6524600	Strong transcription	Fetal Thymus	thymus
20	chr10:6517400-6525000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr10:6517400-6527000	Weak transcription	Brain Substantia Nigra	brain
22	chr10:6517400-6527800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr10:6517600-6539600	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr10:6517600-6541800	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr10:6517800-6525000	Weak transcription	Brain Hippocampus Middle	brain
26	chr10:6518000-6524200	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr10:6518200-6524000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
28	chr10:6518200-6524800	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr10:6518200-6525200	Strong transcription	Thymus	Thymus
30	chr10:6518200-6535400	Weak transcription	Fetal Kidney	kidney
31	chr10:6518200-6556800	Weak transcription	Fetal Intestine Large	intestine
32	chr10:6518400-6524600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr10:6518600-6524800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr10:6518800-6524600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr10:6518800-6525000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr10:6519000-6523600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr10:6519000-6525000	Strong transcription	Primary T cells from cord blood	blood
38	chr10:6519000-6535400	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr10:6519200-6525000	Strong transcription	Dnd41	blood
40	chr10:6519200-6544400	Weak transcription	Spleen	Spleen
41	chr10:6519400-6524200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr10:6519400-6527400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr10:6519600-6521600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr10:6519600-6524000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr10:6519600-6524200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:6519600-6532400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr10:6519800-6525000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr10:6520000-6524000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr10:6520000-6524200	Weak transcription	NHEK	skin
50	chr10:6520000-6535600	Weak transcription	Fetal Intestine Small	intestine

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