Variant report

Variant	rs11144865
Chromosome Location	chr9:78996924-78996925
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:78995453..78997837-chr9:79007820..79009710,2	K562	blood:

Variant related genes	Relation type
ENSG00000135002	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10119532	0.89[GIH][hapmap]
rs10121699	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs10124695	0.80[ASN][1000 genomes]
rs10781361	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10869767	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10869773	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11144864	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144866	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11144871	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11144880	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11144898	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12057052	0.87[ASN][1000 genomes]
rs13288968	0.84[ASN][1000 genomes]
rs13295433	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13302654	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1535845	0.80[ASN][1000 genomes]
rs1961995	0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2002423	0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2251604	0.96[ASN][1000 genomes]
rs2377639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490572	0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2490573	0.98[ASN][1000 genomes]
rs2490574	0.86[ASN][1000 genomes]
rs2490576	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2490579	0.96[ASN][1000 genomes]
rs2490583	0.84[ASN][1000 genomes]
rs2490584	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2490586	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2501920	0.80[ASN][1000 genomes]
rs2501922	0.95[ASN][1000 genomes]
rs2501923	0.96[ASN][1000 genomes]
rs2501925	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2501927	0.96[ASN][1000 genomes]
rs2501928	1.00[ASN][1000 genomes]
rs2501930	0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2501932	0.86[ASN][1000 genomes]
rs2501933	0.98[ASN][1000 genomes]
rs2501935	0.98[ASN][1000 genomes]
rs2501937	0.83[ASN][1000 genomes]
rs2501938	0.83[ASN][1000 genomes]
rs2501939	0.83[ASN][1000 genomes]
rs35837300	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3739516	0.80[CEU][hapmap]
rs3739729	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4372070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4745541	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4745544	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4745549	0.87[AMR][1000 genomes]
rs4745551	0.86[GIH][hapmap]
rs4745552	0.80[CEU][hapmap];0.88[GIH][hapmap]
rs6560517	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6560522	0.95[JPT][hapmap]
rs7847608	0.84[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7849239	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7861089	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7871849	0.89[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11144865	GNA14	cis	parietal	SCAN
rs11144865	VPS13A	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78986600-79008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:78987600-79007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:78988200-79002600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr9:78988200-79003200	Weak transcription	HSMMtube	muscle
5	chr9:78988200-79008400	Weak transcription	Brain Substantia Nigra	brain
6	chr9:78988200-79008400	Weak transcription	Fetal Heart	heart
7	chr9:78988400-78999000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:78988400-78999000	Weak transcription	Spleen	Spleen
9	chr9:78988400-78999600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:78988400-79002200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:78988600-79001000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:78988600-79001000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:78988600-79002400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:78988600-79007800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:78988600-79008200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr9:78988800-78999800	Weak transcription	Brain Anterior Caudate	brain
17	chr9:78988800-79006000	Weak transcription	Brain Angular Gyrus	brain
18	chr9:78988800-79007200	Weak transcription	Brain Hippocampus Middle	brain
19	chr9:78988800-79008400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr9:78989000-78998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:78989000-78999800	Weak transcription	GM12878-XiMat	blood
22	chr9:78989000-79000000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:78989000-79000200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:78989200-78997800	Weak transcription	Ovary	ovary
25	chr9:78989800-78999800	Weak transcription	Aorta	Aorta
26	chr9:78990000-78998600	Weak transcription	Colonic Mucosa	Colon
27	chr9:78990000-79005400	Weak transcription	Small Intestine	intestine
28	chr9:78990200-78999000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:78990200-79007800	Weak transcription	Fetal Brain Male	brain
30	chr9:78990200-79008400	Weak transcription	Right Ventricle	heart
31	chr9:78990400-78998400	Weak transcription	Adipose Nuclei	Adipose
32	chr9:78990400-78998800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr9:78990400-78999000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:78990400-78999200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:78990400-78999200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:78990400-78999200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr9:78990400-78999600	Weak transcription	Left Ventricle	heart
38	chr9:78990400-78999600	Weak transcription	HSMM	muscle
39	chr9:78990400-78999800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:78990400-78999800	Weak transcription	Fetal Muscle Leg	muscle
41	chr9:78990400-79001000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:78990400-79002600	Weak transcription	Esophagus	oesophagus
43	chr9:78990400-79008200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr9:78990400-79008400	Weak transcription	Fetal Kidney	kidney
45	chr9:78990600-78997800	Weak transcription	Liver	Liver
46	chr9:78990600-78999000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr9:78990600-78999000	Weak transcription	Osteobl	bone
48	chr9:78990600-78999600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr9:78990600-78999800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:78990600-78999800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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