Variant report

Variant	rs928604
Chromosome Location	chr10:99180522-99180523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11189213	1.00[CHB][hapmap]
rs11189254	0.82[JPT][hapmap]
rs12245837	0.82[JPT][hapmap]
rs12259524	0.82[JPT][hapmap]
rs17107905	0.91[CHD][hapmap];0.82[JPT][hapmap]
rs17108072	0.82[JPT][hapmap]
rs17112803	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs1889545	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3814552	0.91[CHD][hapmap];0.82[JPT][hapmap]
rs4418736	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4919098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4919110	0.82[JPT][hapmap]
rs6584122	0.89[CEU][hapmap]
rs7089713	0.84[CHD][hapmap]
rs946984	0.82[JPT][hapmap]
rs946987	0.84[CHD][hapmap]
rs964733	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][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	nsv467440	chr10:99134784-99204791	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv552025	chr10:99134784-99204791	Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv2129862	chr10:99180523-99180527	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs928604	C10orf62	cis	cerebellum	SCAN
rs928604	EXOSC1	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99161600-99185200	Weak transcription	Pancreas	Pancrea
2	chr10:99167400-99185200	Weak transcription	Fetal Lung	lung
3	chr10:99167400-99185400	Weak transcription	Gastric	stomach
4	chr10:99167600-99185200	Weak transcription	Fetal Intestine Small	intestine
5	chr10:99167600-99185200	Weak transcription	Left Ventricle	heart
6	chr10:99171400-99185200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:99173200-99182800	Weak transcription	HUVEC	blood vessel
8	chr10:99173800-99182400	Weak transcription	Esophagus	oesophagus
9	chr10:99174000-99185000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:99174200-99183000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr10:99174200-99184800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr10:99174200-99185000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr10:99175000-99182800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr10:99175200-99182200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr10:99175200-99182800	Weak transcription	NH-A	brain
16	chr10:99175200-99182800	Weak transcription	Osteobl	bone
17	chr10:99175400-99185000	Weak transcription	Brain Germinal Matrix	brain
18	chr10:99176600-99183000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:99176600-99185200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr10:99177800-99185200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr10:99178200-99185200	Weak transcription	Ovary	ovary
22	chr10:99178400-99180800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr10:99178400-99185000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr10:99178400-99185200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr10:99178400-99185200	Weak transcription	Right Ventricle	heart
26	chr10:99178400-99185200	Weak transcription	Small Intestine	intestine
27	chr10:99178600-99184800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr10:99178800-99182800	Weak transcription	GM12878-XiMat	blood
29	chr10:99178800-99185400	Weak transcription	Aorta	Aorta
30	chr10:99179000-99184800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr10:99179000-99184800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:99179000-99185200	Weak transcription	Lung	lung
33	chr10:99179200-99180600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr10:99179200-99180800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr10:99179200-99181400	Enhancers	HepG2	liver
36	chr10:99179200-99182400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr10:99179200-99182400	Weak transcription	Fetal Muscle Leg	muscle
38	chr10:99179200-99182800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr10:99179200-99182800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr10:99179200-99182800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr10:99179200-99182800	Weak transcription	A549	lung
42	chr10:99179200-99182800	Weak transcription	HMEC	breast
43	chr10:99179200-99182800	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr10:99179200-99182800	Weak transcription	NHEK	skin
45	chr10:99179200-99183000	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr10:99179200-99183000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr10:99179200-99184600	Weak transcription	Placenta	Placenta
48	chr10:99179200-99184800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr10:99179200-99184800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr10:99179200-99185000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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