Variant report

Variant	rs12784530
Chromosome Location	chr10:97440394-97440395
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97440066..97441614-chr10:97451654..97455031,3	MCF-7	breast:
2	chr10:97438903..97441882-chr10:97445653..97448127,2	K562	blood:

Variant related genes	Relation type
ENSG00000119977	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10882654	0.89[JPT][hapmap]
rs11188410	0.88[JPT][hapmap]
rs11188412	0.88[JPT][hapmap]
rs11188415	0.88[JPT][hapmap]
rs11188418	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11188419	0.88[JPT][hapmap]
rs11188423	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11188428	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11188431	0.88[JPT][hapmap]
rs11188433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188466	0.88[JPT][hapmap]
rs11188469	0.88[JPT][hapmap]
rs11188475	0.88[JPT][hapmap]
rs11188502	1.00[JPT][hapmap]
rs11553577	0.88[JPT][hapmap]
rs12358517	0.88[JPT][hapmap]
rs2275760	0.85[JPT][hapmap]
rs2282305	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3176882	0.88[JPT][hapmap]
rs3181121	0.88[JPT][hapmap]
rs35722210	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3818833	0.88[JPT][hapmap]
rs7073937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7080192	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7090630	0.88[JPT][hapmap]
rs7093453	0.88[JPT][hapmap]
rs7100644	0.88[JPT][hapmap]

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	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12784530	ALDH18A1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97416600-97441000	Weak transcription	Spleen	Spleen
2	chr10:97416800-97441600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:97416800-97442400	Weak transcription	Small Intestine	intestine
4	chr10:97416800-97443400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:97417000-97441000	Weak transcription	HSMMtube	muscle
6	chr10:97417000-97442400	Weak transcription	Aorta	Aorta
7	chr10:97417000-97444200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:97417000-97445200	Weak transcription	Colonic Mucosa	Colon
9	chr10:97417000-97445800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr10:97417000-97445800	Weak transcription	NHLF	lung
11	chr10:97417200-97441000	Weak transcription	Thymus	Thymus
12	chr10:97417200-97441800	Weak transcription	Brain Angular Gyrus	brain
13	chr10:97417200-97442400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr10:97417200-97444400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr10:97417200-97445800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr10:97421800-97441800	Weak transcription	Gastric	stomach
17	chr10:97423000-97452000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:97423600-97441000	Weak transcription	Lung	lung
19	chr10:97423600-97441800	Weak transcription	Esophagus	oesophagus
20	chr10:97424000-97448200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr10:97424200-97440600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr10:97424400-97440800	Weak transcription	Right Ventricle	heart
23	chr10:97424400-97443200	Weak transcription	Pancreas	Pancrea
24	chr10:97425600-97440800	Weak transcription	K562	blood
25	chr10:97427800-97452600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr10:97429600-97441200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr10:97430800-97441000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr10:97431800-97446800	Weak transcription	Fetal Heart	heart
29	chr10:97431800-97450600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr10:97431800-97451200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr10:97432000-97450800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr10:97432800-97452000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr10:97433000-97451800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr10:97433400-97447600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:97433400-97447600	Strong transcription	Adipose Nuclei	Adipose
36	chr10:97433400-97451400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:97433800-97452600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr10:97434000-97452000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr10:97434200-97452000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr10:97434400-97450600	Strong transcription	Dnd41	blood
41	chr10:97434400-97451000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr10:97434400-97451600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:97434400-97452200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr10:97434600-97450400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr10:97434600-97450800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr10:97434600-97451000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr10:97434600-97451600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr10:97434800-97446800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr10:97434800-97451800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr10:97434800-97451800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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