Variant report

Variant	rs11592144
Chromosome Location	chr10:99283062-99283063
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99271315..99274212-chr10:99282293..99285243,2	K562	blood:
2	chr10:99256542..99259693-chr10:99280360..99283727,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155229	Chromatin interaction
ENSG00000165886	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10786352	0.95[CEU][hapmap];0.89[CHD][hapmap];0.87[EUR][1000 genomes]
rs10882947	0.95[CEU][hapmap];0.89[CHD][hapmap]
rs10882950	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs10882951	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs10882952	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10882953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882954	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11189247	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11189255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11189258	0.82[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap]
rs11189268	0.89[ASN][1000 genomes]
rs11592973	0.81[CEU][hapmap];0.89[CHD][hapmap]
rs34642355	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35483267	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074482	0.86[TSI][hapmap]
rs7077917	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7341998	0.82[CEU][hapmap];0.93[GIH][hapmap];0.83[TSI][hapmap]
rs7906491	0.96[ASN][1000 genomes]
rs872106	0.81[CEU][hapmap];0.89[CHD][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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11592144	LOXL4	cis	cerebellum	SCAN
rs11592144	ADAMDEC1	trans	lymphoblastoid	seeQTL
rs11592144	TBC1D30	trans	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99270800-99286200	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr10:99273800-99283200	Enhancers	Fetal Muscle Leg	muscle
3	chr10:99273800-99283200	Enhancers	Left Ventricle	heart
4	chr10:99274200-99285000	Enhancers	Right Ventricle	heart
5	chr10:99275000-99293800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:99276000-99284400	Weak transcription	HepG2	liver
7	chr10:99277800-99301800	Weak transcription	Gastric	stomach
8	chr10:99278000-99302600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr10:99278200-99298800	Weak transcription	Aorta	Aorta
10	chr10:99278400-99289600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr10:99278400-99301800	Weak transcription	Spleen	Spleen
12	chr10:99278600-99284400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr10:99278600-99300200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr10:99278800-99284400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr10:99279000-99284400	Weak transcription	Ovary	ovary
16	chr10:99279400-99284600	Weak transcription	Adipose Nuclei	Adipose
17	chr10:99279600-99284000	Enhancers	Right Atrium	heart
18	chr10:99279800-99283800	Weak transcription	Brain Hippocampus Middle	brain
19	chr10:99279800-99284600	Weak transcription	Brain Angular Gyrus	brain
20	chr10:99279800-99287200	Enhancers	Lung	lung
21	chr10:99280200-99284600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr10:99281200-99291400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr10:99281400-99302200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr10:99281800-99283600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr10:99282200-99283800	Weak transcription	Psoas Muscle	Psoas
26	chr10:99282200-99284400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr10:99282200-99284400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr10:99282200-99289400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:99282200-99289600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr10:99282200-99301800	Weak transcription	Pancreas	Pancrea
31	chr10:99282400-99284400	Weak transcription	Brain Substantia Nigra	brain
32	chr10:99282400-99291200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr10:99282400-99298200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr10:99282600-99284400	Weak transcription	Brain Anterior Caudate	brain
35	chr10:99282800-99283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr10:99282800-99284400	Weak transcription	Esophagus	oesophagus
37	chr10:99282800-99292800	Weak transcription	HSMMtube	muscle
38	chr10:99282800-99299400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr10:99283000-99284400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr10:99283000-99284600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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