Variant report

Variant	rs12038373
Chromosome Location	chr1:225792814-225792815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225792350..225796305-chr1:225796696..225799620,4	MCF-7	breast:
2	chr1:225782318..225785291-chr1:225791224..225794186,2	MCF-7	breast:
3	chr1:225784703..225788501-chr1:225791324..225793418,3	K562	blood:
4	chr1:225791587..225793375-chr1:225840069..225842587,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10449249	0.89[EUR][1000 genomes]
rs11377355	0.89[EUR][1000 genomes]
rs12022013	1.00[CEU][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs12031651	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12037289	0.97[EUR][1000 genomes]
rs12042273	0.97[EUR][1000 genomes]
rs16845000	1.00[CEU][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2184778	1.00[CEU][hapmap];0.94[CHD][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2185531	0.92[EUR][1000 genomes]
rs2296880	0.92[EUR][1000 genomes]
rs3766931	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3795443	0.84[CHD][hapmap]
rs4129816	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56169721	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58696877	0.83[EUR][1000 genomes]
rs61333083	0.86[EUR][1000 genomes]
rs6674621	1.00[CEU][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs74149835	0.94[EUR][1000 genomes]
rs74149844	0.97[EUR][1000 genomes]
rs7415548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7543444	1.00[CEU][hapmap];0.94[CHD][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]

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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12038373	LBR	cis	Artery Tibial	GTEx
rs12038373	LBR	cis	Esophagus Muscularis	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225748800-225799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:225768800-225805600	Weak transcription	Aorta	Aorta
4	chr1:225774800-225793200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:225776400-225797200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:225777000-225793400	Weak transcription	Pancreas	Pancrea
7	chr1:225778600-225794200	Weak transcription	Brain Substantia Nigra	brain
8	chr1:225780200-225794200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:225780800-225815400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:225781000-225825400	Weak transcription	Fetal Stomach	stomach
11	chr1:225781200-225793200	Weak transcription	Ovary	ovary
12	chr1:225782000-225795000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:225782400-225795200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:225782400-225806200	Weak transcription	Right Ventricle	heart
15	chr1:225784200-225807800	Weak transcription	Fetal Brain Male	brain
16	chr1:225784800-225793200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:225785200-225800000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:225785400-225794600	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:225787800-225794600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:225788000-225793000	Weak transcription	Fetal Intestine Small	intestine
21	chr1:225788400-225795000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:225788400-225795200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:225788400-225796200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:225788600-225794800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:225789800-225793000	Enhancers	Stomach Mucosa	stomach
26	chr1:225789800-225793600	Enhancers	Fetal Heart	heart
27	chr1:225790200-225793200	Enhancers	Osteobl	bone
28	chr1:225790400-225793000	Enhancers	NHEK	skin
29	chr1:225790400-225793200	Weak transcription	Right Atrium	heart
30	chr1:225790400-225793400	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr1:225790400-225793600	Enhancers	Colon Smooth Muscle	Colon
32	chr1:225790400-225794800	Weak transcription	Brain Germinal Matrix	brain
33	chr1:225791000-225793000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:225791200-225798800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:225791400-225793400	Weak transcription	Small Intestine	intestine
36	chr1:225791400-225796600	Weak transcription	Brain Angular Gyrus	brain
37	chr1:225791600-225793000	Enhancers	HUVEC	blood vessel
38	chr1:225791600-225795000	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:225791600-225795200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:225791600-225795400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:225791600-225796600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:225791600-225799600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:225791600-225802000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:225791800-225794600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:225791800-225794600	Weak transcription	HSMMtube	muscle
46	chr1:225792000-225793000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:225792000-225793000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:225792000-225793400	Enhancers	A549	lung
49	chr1:225792000-225794400	Weak transcription	Fetal Lung	lung
50	chr1:225792000-225794600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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