Variant report

Variant	rs697846
Chromosome Location	chr1:226817699-226817700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12076436	0.85[CHD][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap]
rs12739464	0.84[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap]
rs12747353	0.93[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes]
rs3738722	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3754378	0.93[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs708760	0.88[AFR][1000 genomes]

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	nsv470779	chr1:226778432-226833304	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs697846	WNT3A	cis	cerebellum	SCAN
rs697846	TMEM63A	cis	parietal	SCAN
rs697846	PRSS38	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226806200-226825800	Weak transcription	Right Atrium	heart
2	chr1:226810600-226822600	Weak transcription	Gastric	stomach
3	chr1:226812400-226817800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:226814200-226819400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr1:226814200-226820600	Weak transcription	Right Ventricle	heart
6	chr1:226814200-226821400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:226814200-226823600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:226814200-226837600	Weak transcription	HUVEC	blood vessel
9	chr1:226814400-226817800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:226814400-226819200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:226814400-226819400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:226814400-226820200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:226814400-226821600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:226814600-226820000	Weak transcription	Dnd41	blood
15	chr1:226814600-226824200	Weak transcription	Brain Angular Gyrus	brain
16	chr1:226814600-226824800	Weak transcription	Liver	Liver
17	chr1:226814800-226819400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:226814800-226819800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:226814800-226820400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:226814800-226820600	Weak transcription	Brain Anterior Caudate	brain
21	chr1:226814800-226821200	Weak transcription	Adipose Nuclei	Adipose
22	chr1:226814800-226821600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:226814800-226830400	Strong transcription	Thymus	Thymus
24	chr1:226814800-226834800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:226814800-226840600	Weak transcription	Small Intestine	intestine
26	chr1:226815000-226818800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:226815000-226819200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:226815000-226819400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:226815000-226819400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:226815000-226819600	Weak transcription	Colonic Mucosa	Colon
31	chr1:226815000-226819800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:226815000-226820000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:226815000-226820000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:226815000-226820000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:226815000-226820400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:226815000-226821600	Weak transcription	Esophagus	oesophagus
37	chr1:226815000-226823800	Weak transcription	Ovary	ovary
38	chr1:226815200-226821400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:226815400-226818600	Weak transcription	Primary B cells from cord blood	blood
40	chr1:226815400-226818800	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:226816000-226819800	Weak transcription	GM12878-XiMat	blood
42	chr1:226816000-226820000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:226816000-226820400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:226816200-226819200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr1:226816400-226819600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:226816400-226820200	Strong transcription	Primary T cells from cord blood	blood
47	chr1:226816400-226820600	Strong transcription	Fetal Thymus	thymus
48	chr1:226816800-226818000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:226816800-226818800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:226816800-226819800	Weak transcription	Brain Germinal Matrix	brain

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