Variant report

Variant	rs2554856
Chromosome Location	chr12:51387438-51387439
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	chr12:51385408..51389476-chr12:51420028..51421870,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10783410	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876123	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11169657	0.81[EUR][1000 genomes]
rs12809226	0.89[ASN][1000 genomes]
rs12823317	0.89[ASN][1000 genomes]
rs149411	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1632791	0.81[EUR][1000 genomes]
rs224575	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2359187	0.87[ASN][1000 genomes]
rs2544019	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs319931	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs319936	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs319939	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs706805	0.81[EUR][1000 genomes]
rs7961626	0.86[EUR][1000 genomes]
rs829017	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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
rs2554856	LETMD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51378000-51401800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr12:51378400-51391200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:51378600-51393200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:51378600-51399000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:51378800-51396000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:51379400-51396000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:51379400-51396200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:51379600-51389200	Weak transcription	Fetal Heart	heart
9	chr12:51379600-51395600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:51379800-51391000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:51379800-51394600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:51379800-51396400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:51380000-51396200	Strong transcription	Dnd41	blood
14	chr12:51380200-51391400	Strong transcription	Fetal Muscle Trunk	muscle
15	chr12:51380200-51396400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:51380200-51396600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:51380200-51401800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr12:51380200-51402200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr12:51380400-51391400	Strong transcription	Brain Germinal Matrix	brain
20	chr12:51380400-51396200	Strong transcription	Fetal Brain Female	brain
21	chr12:51380400-51396200	Strong transcription	Placenta	Placenta
22	chr12:51380600-51390800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:51380600-51399600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:51380800-51391600	Strong transcription	Left Ventricle	heart
25	chr12:51381200-51391200	Strong transcription	Brain Hippocampus Middle	brain
26	chr12:51381200-51391400	Strong transcription	Colon Smooth Muscle	Colon
27	chr12:51381200-51392200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr12:51381200-51395800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr12:51381200-51402200	Strong transcription	Fetal Thymus	thymus
30	chr12:51381200-51402200	Weak transcription	Psoas Muscle	Psoas
31	chr12:51381200-51402400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr12:51381200-51403000	Strong transcription	Fetal Muscle Leg	muscle
33	chr12:51381400-51391000	Strong transcription	Rectal Smooth Muscle	rectum
34	chr12:51381400-51394200	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr12:51381400-51396400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr12:51381400-51403000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr12:51381600-51391000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr12:51381800-51391200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr12:51381800-51391400	Strong transcription	Brain Cingulate Gyrus	brain
40	chr12:51381800-51391600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:51381800-51401600	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr12:51381800-51401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:51381800-51402400	Strong transcription	Liver	Liver
44	chr12:51382000-51390800	Strong transcription	Right Ventricle	heart
45	chr12:51382000-51391400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:51382000-51391600	Strong transcription	Thymus	Thymus
47	chr12:51382000-51394600	Strong transcription	Lung	lung
48	chr12:51382000-51395800	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr12:51382000-51396400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr12:51382000-51402000	Strong transcription	Fetal Stomach	stomach

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