Variant report

Variant	rs2689700
Chromosome Location	chr10:95946520-95946521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs17417407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17515035	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1776942	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1776946	0.95[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2689705	0.95[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2764339	0.81[EUR][1000 genomes]
rs2764345	0.81[EUR][1000 genomes]
rs2797982	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2797985	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3861986	0.93[CEU][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.84[ASN][1000 genomes]
rs4277037	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58730112	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60208943	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61886304	0.81[AFR][1000 genomes]
rs61886305	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61886306	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61886307	0.82[ASN][1000 genomes]
rs61886308	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7082818	0.81[EUR][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	nsv1036676	chr10:95851376-96103876	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv3348296	chr10:95946461-95946660	Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2689700	C10orf28	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95924800-95947200	Weak transcription	Aorta	Aorta
2	chr10:95929000-95954200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:95929200-95966800	Weak transcription	Pancreas	Pancrea
4	chr10:95931600-95953000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr10:95931800-95952600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr10:95932000-95948800	Weak transcription	Gastric	stomach
7	chr10:95932000-95953000	Weak transcription	Colonic Mucosa	Colon
8	chr10:95932600-95968000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr10:95932800-95954200	Weak transcription	Fetal Brain Female	brain
10	chr10:95933000-95953000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr10:95933000-95954200	Weak transcription	Right Atrium	heart
12	chr10:95933000-95972600	Weak transcription	Fetal Intestine Large	intestine
13	chr10:95939200-95952800	Weak transcription	Ovary	ovary
14	chr10:95940600-95952800	Weak transcription	Fetal Lung	lung
15	chr10:95941200-95979800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr10:95941600-95947200	Weak transcription	Fetal Stomach	stomach
17	chr10:95943400-95973800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr10:95943800-95952800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr10:95944000-95952600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr10:95944000-95952600	Weak transcription	A549	lung
21	chr10:95944000-95952600	Weak transcription	NH-A	brain
22	chr10:95944200-95959800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr10:95944400-95952600	Weak transcription	Fetal Muscle Leg	muscle
24	chr10:95944600-95947400	Weak transcription	Fetal Intestine Small	intestine
25	chr10:95945000-95952800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr10:95945200-95951200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr10:95946200-95947200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr10:95946200-95947400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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