Variant report

Variant	rs11471
Chromosome Location	chr10:45499799-45499800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CCNT2	chr10:45499678-45499878	K562	blood:	n/a	n/a
2	POLR2A	chr10:45499672-45503840	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:45495742..45497934-chr10:45498787..45500751,2	MCF-7	breast:
2	chr10:45499571..45502259-chr10:45742998..45745677,2	K562	blood:

Variant related genes	Relation type
C10orf25	TF binding region
ENSG00000165512	Chromatin interaction
ENSG00000165511	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10751364	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10751365	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10793581	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10900161	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1343628	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2095089	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2311846	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3740090	0.84[AMR][1000 genomes]
rs3901394	0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6593456	0.80[AFR][1000 genomes]
rs7898523	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs979528	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv831848	chr10:45490176-45667670	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11471	LOC84856	cis	cerebellum	SCAN
rs11471	RASGEF1A	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45497000-45511000	Weak transcription	Gastric	stomach
2	chr10:45497200-45500200	Weak transcription	Lung	lung
3	chr10:45497200-45504000	Weak transcription	Esophagus	oesophagus
4	chr10:45497400-45501200	Weak transcription	Aorta	Aorta
5	chr10:45497400-45501400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:45497400-45503800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr10:45497400-45504000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr10:45497400-45504000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr10:45497600-45499800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr10:45497600-45500200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr10:45497600-45502800	Weak transcription	Fetal Brain Male	brain
12	chr10:45497600-45503800	Weak transcription	Brain Substantia Nigra	brain
13	chr10:45497600-45504000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr10:45497800-45500600	ZNF genes & repeats	Primary B cells from cord blood	blood
15	chr10:45497800-45500600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr10:45497800-45502200	Weak transcription	Right Ventricle	heart
17	chr10:45497800-45504000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr10:45498000-45500000	ZNF genes & repeats	Primary T cells from cord blood	blood
19	chr10:45498000-45500000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
20	chr10:45498000-45500200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:45498200-45500600	ZNF genes & repeats	GM12878-XiMat	blood
22	chr10:45498200-45503800	Weak transcription	Colon Smooth Muscle	Colon
23	chr10:45498200-45503800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr10:45498200-45504000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr10:45498400-45500200	Weak transcription	Osteobl	bone
26	chr10:45498400-45500400	Genic enhancers	Primary hematopoietic stem cells	blood
27	chr10:45498400-45500600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
28	chr10:45498400-45501200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr10:45498400-45503800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr10:45498600-45499800	Genic enhancers	Dnd41	blood
31	chr10:45498600-45500400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr10:45498600-45500400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr10:45498600-45500800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
34	chr10:45498600-45501400	Strong transcription	Fetal Lung	lung
35	chr10:45498800-45499800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:45498800-45499800	Strong transcription	Placenta	Placenta
37	chr10:45498800-45499800	Strong transcription	A549	lung
38	chr10:45498800-45499800	ZNF genes & repeats	NH-A	brain
39	chr10:45498800-45499800	Strong transcription	NHDF-Ad	bronchial
40	chr10:45498800-45500000	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr10:45498800-45500000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:45498800-45500000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
43	chr10:45498800-45500000	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr10:45498800-45500000	ZNF genes & repeats	HMEC	breast
45	chr10:45498800-45500400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr10:45498800-45500400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
47	chr10:45498800-45500400	Strong transcription	Rectal Smooth Muscle	rectum
48	chr10:45498800-45500600	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr10:45498800-45500600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr10:45498800-45500600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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