Variant report

Variant	rs2630370
Chromosome Location	chr12:51337257-51337258
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	chr12:51336604..51339299-chr12:51340457..51342342,2	MCF-7	breast:
2	chr12:51329075..51331156-chr12:51335515..51338529,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10783409	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1095999	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169657	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12424509	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1632791	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17125111	0.88[ASN][1000 genomes]
rs224448	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs224572	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2554863	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2630371	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs370462	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs427020	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4768947	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs706805	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7977740	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829015	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs829025	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2630370	LETMD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51319400-51346200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
3	chr12:51328800-51378000	Weak transcription	Brain Substantia Nigra	brain
4	chr12:51329200-51341600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr12:51329600-51373600	Weak transcription	Left Ventricle	heart
6	chr12:51331400-51378400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:51331600-51338000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:51331600-51373800	Weak transcription	Pancreas	Pancrea
9	chr12:51331800-51342800	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:51331800-51343000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr12:51331800-51353800	Weak transcription	Primary T cells from cord blood	blood
12	chr12:51331800-51382000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:51331800-51382000	Weak transcription	Ovary	ovary
14	chr12:51332000-51346400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:51332400-51343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:51332400-51346200	Weak transcription	Fetal Intestine Small	intestine
17	chr12:51332400-51346200	Weak transcription	Fetal Muscle Leg	muscle
18	chr12:51332400-51346200	Weak transcription	Fetal Stomach	stomach
19	chr12:51332600-51346400	Weak transcription	Brain Angular Gyrus	brain
20	chr12:51332600-51354400	Weak transcription	Thymus	Thymus
21	chr12:51332600-51365000	Weak transcription	Fetal Brain Female	brain

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