Variant report

Variant	rs10512231
Chromosome Location	chr9:96945748-96945749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96943921..96946821-chr9:96947982..96950934,2	MCF-7	breast:
2	chr9:96858833..96861735-chr9:96944084..96946628,2	K562	blood:
3	chr9:96762359..96764035-chr9:96943994..96946319,2	K562	blood:
4	chr9:96927843..96930054-chr9:96943540..96946724,4	MCF-7	breast:
5	chr9:96940341..96943331-chr9:96943637..96946113,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199133	Chromatin interaction
ENSG00000269946	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10114341	0.83[CHD][hapmap]
rs10118003	0.83[CHD][hapmap]
rs10993068	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[ASN][1000 genomes]
rs10993069	0.93[ASN][1000 genomes]
rs10993090	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10993094	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11788788	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12336926	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12337981	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12338333	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12338885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12339587	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12341175	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12345069	0.86[AFR][1000 genomes]
rs12347752	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13295163	0.93[ASN][1000 genomes]
rs13439971	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13440059	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1421135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34582118	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34765284	0.89[ASN][1000 genomes]
rs36044301	0.93[ASN][1000 genomes]
rs55881323	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56006511	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62575976	0.93[ASN][1000 genomes]
rs62575977	0.93[ASN][1000 genomes]
rs62578777	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62578780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578801	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7037996	0.93[ASN][1000 genomes]
rs7041934	0.93[ASN][1000 genomes]
rs7864156	0.93[ASN][1000 genomes]
rs7868381	0.93[ASN][1000 genomes]
rs7871468	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs7872931	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[LWK][hapmap];0.86[MKK][hapmap];0.86[AFR][1000 genomes]
rs7873928	0.93[ASN][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	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
2	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases
3	esv3394266	chr9:96935210-97045514	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	195 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10512231	HIATL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96929800-96948400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:96931400-96965600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:96937200-96959400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:96937800-96946600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:96938200-96949000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:96938400-96947400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:96939400-96948400	Weak transcription	Brain Germinal Matrix	brain
8	chr9:96939600-96947200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:96939600-96947600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:96939600-96948000	Weak transcription	Fetal Brain Female	brain
11	chr9:96939600-96949400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:96939600-96950600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr9:96939800-96946800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:96939800-96946800	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr9:96939800-96947200	Weak transcription	Esophagus	oesophagus
16	chr9:96939800-96947400	Strong transcription	Osteobl	bone
17	chr9:96939800-96948400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr9:96939800-96960800	Weak transcription	NHDF-Ad	bronchial
19	chr9:96940000-96946800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr9:96940000-96949200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr9:96940400-96947800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr9:96940400-96955600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:96940600-96947200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:96940800-96950400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr9:96941000-96945800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:96941200-96946800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr9:96941400-96959400	Weak transcription	Spleen	Spleen
28	chr9:96941600-96947600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr9:96941800-96947200	Weak transcription	Dnd41	blood
30	chr9:96941800-96947200	Strong transcription	HSMM	muscle
31	chr9:96941800-96947600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr9:96942000-96946000	Strong transcription	Thymus	Thymus
33	chr9:96942000-96947200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:96942200-96950000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr9:96942200-96950600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr9:96942400-96947400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr9:96942400-96947600	Weak transcription	HepG2	liver
38	chr9:96942400-96948400	Weak transcription	Fetal Lung	lung
39	chr9:96942400-96949400	Weak transcription	A549	lung
40	chr9:96942400-96949800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr9:96942400-96953200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr9:96942400-96957600	Weak transcription	Colon Smooth Muscle	Colon
43	chr9:96942400-96964000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr9:96942600-96945800	Strong transcription	Primary hematopoietic stem cells	blood
45	chr9:96942600-96946000	Weak transcription	NH-A	brain
46	chr9:96943000-96948600	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr9:96943000-96952200	Weak transcription	HMEC	breast
48	chr9:96943400-96945800	Genic enhancers	GM12878-XiMat	blood
49	chr9:96943400-96949400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:96943800-96947200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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