Variant report

Variant	rs12031651
Chromosome Location	chr1:225726285-225726286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225724327..225726333-chr1:226183688..226185527,2	MCF-7	breast:
2	chr1:225724969..225726561-chr1:225797392..225799589,2	MCF-7	breast:
3	chr1:225725972..225727966-chr1:225729747..225732375,2	K562	blood:
4	chr1:225724215..225726983-chr1:226108723..226110957,2	K562	blood:
5	chr1:225710178..225712804-chr1:225725363..225728293,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143811	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10449249	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10915829	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11377355	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12022013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12026034	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12031208	0.85[ASN][1000 genomes]
rs12037289	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12038373	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12042273	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12042698	0.82[ASN][1000 genomes]
rs12239415	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1340870	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1340871	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1340872	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16845000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2184778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2185531	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296880	0.86[EUR][1000 genomes]
rs2297747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs28620013	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3766931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3795443	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4129816	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs487591	0.82[YRI][hapmap]
rs55751087	0.82[ASN][1000 genomes]
rs56169721	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58269599	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59912270	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61333083	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6674621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681559	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6684314	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6684956	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6694938	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs74146931	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs74146994	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs74149835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74149844	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7415548	0.94[EUR][1000 genomes]
rs7543444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12031651	LBR	cis	Artery Tibial	GTEx
rs12031651	LBR	cis	Esophagus Muscularis	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225700000-225726400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:225700000-225726400	Weak transcription	HMEC	breast
3	chr1:225701400-225727200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:225701400-225744400	Weak transcription	HUVEC	blood vessel
5	chr1:225701400-225747000	Weak transcription	Hela-S3	cervix
6	chr1:225705600-225747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:225705800-225726600	Weak transcription	NHEK	skin
8	chr1:225707200-225726600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:225707200-225755000	Weak transcription	Gastric	stomach
10	chr1:225707400-225726600	Weak transcription	Brain Angular Gyrus	brain
11	chr1:225711400-225726600	Weak transcription	Fetal Brain Female	brain
12	chr1:225712400-225729600	Weak transcription	Right Ventricle	heart
13	chr1:225714800-225729600	Weak transcription	Ovary	ovary
14	chr1:225716800-225726400	Weak transcription	Left Ventricle	heart
15	chr1:225716800-225726400	Weak transcription	Psoas Muscle	Psoas
16	chr1:225717600-225726600	Weak transcription	NHDF-Ad	bronchial
17	chr1:225717600-225732000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:225717600-225744400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:225717800-225729600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:225717800-225744400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:225717800-225745000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:225717800-225747400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:225717800-225747400	Weak transcription	Fetal Stomach	stomach
24	chr1:225717800-225758200	Weak transcription	HepG2	liver
25	chr1:225718200-225727000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:225718400-225726800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:225718400-225732600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:225718400-225756400	Weak transcription	NHLF	lung
29	chr1:225718800-225726600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:225719000-225728000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:225719800-225727000	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr1:225719800-225730400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr1:225720000-225726600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:225721000-225728600	Weak transcription	Fetal Brain Male	brain
35	chr1:225721400-225726600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:225721400-225726600	Weak transcription	HSMMtube	muscle
37	chr1:225721600-225735200	Weak transcription	HSMM	muscle
38	chr1:225721800-225726600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:225722000-225726400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:225722000-225726600	Weak transcription	Fetal Heart	heart
41	chr1:225722000-225727200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:225722000-225729800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:225722800-225726600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:225722800-225726600	Weak transcription	A549	lung
45	chr1:225722800-225728000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:225722800-225747600	Weak transcription	Fetal Intestine Small	intestine
47	chr1:225723000-225728200	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:225723200-225739600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:225723400-225735200	Weak transcription	NH-A	brain
50	chr1:225723600-225726600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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