Variant report

Variant	rs10828779
Chromosome Location	chr10:18787821-18787822
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11014166	0.86[CHB][hapmap]
rs12257502	0.86[CHB][hapmap]
rs12765864	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1409205	0.82[JPT][hapmap]
rs1570937	1.00[JPT][hapmap]
rs16917367	1.00[CHB][hapmap]
rs16917369	1.00[CHB][hapmap]
rs16917375	1.00[CHB][hapmap]
rs4748472	0.89[ASW][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs7069531	0.86[CHB][hapmap]
rs9943388	0.86[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10828779	CACNB2	cis	cerebellum	SCAN
rs10828779	C10orf140	cis	cerebellum	SCAN
rs10828779	DCLRE1C	cis	cerebellum	SCAN
rs10828779	NSUN6	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18732400-18801600	Weak transcription	Pancreas	Pancrea
2	chr10:18775600-18800600	Weak transcription	Fetal Intestine Large	intestine
3	chr10:18776200-18809400	Weak transcription	Right Ventricle	heart
4	chr10:18776200-18812200	Weak transcription	Right Atrium	heart
5	chr10:18778600-18818200	Weak transcription	Fetal Intestine Small	intestine
6	chr10:18779600-18803200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr10:18780600-18788200	Weak transcription	Left Ventricle	heart
8	chr10:18781000-18803200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr10:18785400-18808400	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:18785600-18789400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:18786000-18789600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr10:18786000-18794600	Weak transcription	Aorta	Aorta
13	chr10:18786600-18790000	Enhancers	Fetal Heart	heart
14	chr10:18786800-18788000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr10:18786800-18802000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr10:18787000-18788000	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr10:18787000-18788000	Enhancers	Brain Substantia Nigra	brain
18	chr10:18787000-18788200	Enhancers	Fetal Lung	lung
19	chr10:18787200-18788200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr10:18787200-18788400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:18787400-18788000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr10:18787400-18790400	Weak transcription	Brain Anterior Caudate	brain
23	chr10:18787400-18807400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:18787400-18808200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr10:18787400-18810200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr10:18787600-18788000	Enhancers	Fetal Stomach	stomach
27	chr10:18787600-18788400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr10:18787600-18789400	Weak transcription	Brain Hippocampus Middle	brain
29	chr10:18787600-18794600	Weak transcription	Ovary	ovary
30	chr10:18787600-18803200	Weak transcription	Brain Cingulate Gyrus	brain

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