Variant report

Variant	rs6742047
Chromosome Location	chr2:99531460-99531461
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99524623..99526432-chr2:99530090..99532689,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10172158	0.81[AMR][1000 genomes]
rs10192266	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11123755	0.81[AMR][1000 genomes]
rs11123756	0.82[EUR][1000 genomes]
rs12474283	0.85[AMR][1000 genomes]
rs12478574	0.81[EUR][1000 genomes]
rs12712038	0.81[AMR][1000 genomes]
rs12712040	0.81[EUR][1000 genomes]
rs12712041	0.85[AMR][1000 genomes]
rs12712042	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712043	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13004700	0.84[AMR][1000 genomes]
rs13005124	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13006398	0.83[EUR][1000 genomes]
rs13011428	0.85[AMR][1000 genomes]
rs13024838	0.88[EUR][1000 genomes]
rs13025913	0.83[AMR][1000 genomes]
rs13028500	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1581251	0.81[AMR][1000 genomes]
rs1607256	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17758170	0.88[EUR][1000 genomes]
rs1878589	0.86[EUR][1000 genomes]
rs1949424	0.84[EUR][1000 genomes]
rs1962029	0.82[EUR][1000 genomes]
rs1976766	0.83[AMR][1000 genomes]
rs2048949	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4311103	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4499468	0.81[EUR][1000 genomes]
rs4553869	0.82[EUR][1000 genomes]
rs4850889	0.85[AMR][1000 genomes]
rs4850890	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4851167	0.81[AMR][1000 genomes]
rs4851170	0.81[AMR][1000 genomes]
rs4851171	0.80[AMR][1000 genomes]
rs4851173	0.85[AMR][1000 genomes]
rs4851174	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851175	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851176	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851177	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56125264	0.82[AMR][1000 genomes]
rs6419564	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6542841	0.81[EUR][1000 genomes]
rs6542843	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6542845	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6704682	0.82[EUR][1000 genomes]
rs6714243	0.81[AMR][1000 genomes]
rs6724477	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739176	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6739503	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6741166	0.88[EUR][1000 genomes]
rs6752025	0.86[EUR][1000 genomes]
rs6757098	0.81[EUR][1000 genomes]
rs6760065	0.81[EUR][1000 genomes]
rs7423519	0.88[EUR][1000 genomes]
rs7565510	0.82[EUR][1000 genomes]
rs7565819	0.88[EUR][1000 genomes]
rs7588441	0.88[EUR][1000 genomes]
rs7593332	0.84[EUR][1000 genomes]
rs883773	0.82[EUR][1000 genomes]
rs908672	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs925887	0.85[AMR][1000 genomes]

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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv874697	chr2:99520608-99558970	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6742047	LIPT1	cis	Esophagus Mucosa	GTEx
rs6742047	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99524400-99534400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:99524600-99532400	Enhancers	Pancreas	Pancrea
3	chr2:99526400-99534200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:99526600-99533400	Weak transcription	Left Ventricle	heart
5	chr2:99527200-99532000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr2:99527200-99533600	Enhancers	Esophagus	oesophagus
7	chr2:99528000-99534000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:99528200-99534400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:99528400-99532000	Enhancers	Gastric	stomach
10	chr2:99529200-99534000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:99529200-99534200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:99529400-99534000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:99529600-99533200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:99529800-99532600	Weak transcription	HUVEC	blood vessel
15	chr2:99529800-99533200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr2:99530000-99532200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:99530000-99532600	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr2:99530200-99532000	Enhancers	Brain Angular Gyrus	brain
19	chr2:99530200-99532200	Weak transcription	NHDF-Ad	bronchial
20	chr2:99530200-99534000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:99530400-99532200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:99530400-99532200	Weak transcription	NH-A	brain
23	chr2:99530400-99532400	Weak transcription	Brain Anterior Caudate	brain
24	chr2:99530400-99533800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:99530400-99534400	Enhancers	HMEC	breast
26	chr2:99530600-99532200	Weak transcription	HSMMtube	muscle
27	chr2:99530600-99532200	Weak transcription	Osteobl	bone
28	chr2:99530600-99533400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:99530800-99531600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:99530800-99531600	Weak transcription	Lung	lung
31	chr2:99530800-99532200	Weak transcription	Spleen	Spleen
32	chr2:99530800-99532400	Weak transcription	Brain Germinal Matrix	brain
33	chr2:99530800-99532600	Weak transcription	Fetal Brain Male	brain
34	chr2:99531000-99531600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:99531000-99532200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:99531000-99532400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:99531000-99533400	Weak transcription	Fetal Brain Female	brain
38	chr2:99531200-99531600	Weak transcription	NHEK	skin
39	chr2:99531200-99531800	Enhancers	Fetal Lung	lung
40	chr2:99531200-99531800	Enhancers	Right Ventricle	heart
41	chr2:99531200-99532200	Weak transcription	A549	lung
42	chr2:99531200-99534400	Enhancers	HSMM	muscle
43	chr2:99531200-99539000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:99531400-99532000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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