Variant report

Variant	rs500766
Chromosome Location	chr10:6550590-6550591
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	chr10:6546427..6548106-chr10:6549614..6551845,2	K562	blood:
2	chr10:6545334..6548106-chr10:6549054..6551114,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2387407	0.82[JPT][hapmap]
rs519349	1.00[CEU][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs521153	1.00[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs563798	0.85[JPT][hapmap]
rs586355	0.85[JPT][hapmap]
rs591397	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs627715	0.85[JPT][hapmap]
rs667254	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv5687	chr10:6537209-6556751	Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs500766	TUBAL3	cis	parietal	SCAN
rs500766	AKR1CL1	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6499200-6562000	Weak transcription	Brain Anterior Caudate	brain
2	chr10:6501800-6557000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:6510000-6572000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr10:6517200-6557800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:6518200-6556800	Weak transcription	Fetal Intestine Large	intestine
6	chr10:6526600-6553000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr10:6529000-6552800	Weak transcription	Lung	lung
8	chr10:6530400-6552600	Weak transcription	K562	blood
9	chr10:6533800-6552800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr10:6535400-6553400	Weak transcription	Gastric	stomach
11	chr10:6536600-6552800	Weak transcription	Fetal Intestine Small	intestine
12	chr10:6537400-6552800	Weak transcription	Fetal Stomach	stomach
13	chr10:6537600-6552600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr10:6538200-6552800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr10:6540800-6552200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr10:6540800-6552800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr10:6540800-6556600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr10:6541400-6551000	Strong transcription	Primary hematopoietic stem cells	blood
19	chr10:6541400-6552800	Weak transcription	Fetal Muscle Leg	muscle
20	chr10:6541600-6555200	Strong transcription	Primary T cells from cord blood	blood
21	chr10:6542000-6553000	Strong transcription	Fetal Thymus	thymus
22	chr10:6543000-6555000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr10:6543200-6554600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr10:6544200-6552800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr10:6544600-6552800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:6544600-6553000	Weak transcription	Pancreas	Pancrea
27	chr10:6544600-6558200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr10:6545200-6552800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr10:6545200-6554800	Weak transcription	Psoas Muscle	Psoas
30	chr10:6546000-6550800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr10:6546400-6552800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:6546800-6552800	Weak transcription	NHEK	skin
33	chr10:6546800-6561200	Weak transcription	HMEC	breast
34	chr10:6547200-6554200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr10:6547400-6551200	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr10:6547600-6552200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr10:6548000-6552800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr10:6548600-6550600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr10:6548600-6550600	Enhancers	Brain Hippocampus Middle	brain
40	chr10:6548600-6554800	Strong transcription	Dnd41	blood
41	chr10:6548800-6550800	Strong transcription	Thymus	Thymus
42	chr10:6549200-6550600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
43	chr10:6549200-6550600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr10:6549200-6550600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr10:6549200-6550800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr10:6549200-6551200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr10:6549200-6552600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr10:6549400-6553200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr10:6549600-6552600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr10:6549800-6562400	Weak transcription	Brain Cingulate Gyrus	brain

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