Variant report

Variant	rs224448
Chromosome Location	chr12:51391334-51391335
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:51391294-51391341	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51389215..51392143-chr12:51440341..51442387,3	MCF-7	breast:
2	chr12:51383022..51385187-chr12:51389944..51392124,2	MCF-7	breast:
3	chr12:51389653..51392226-chr12:51393368..51395789,3	MCF-7	breast:
4	chr12:51390934..51393083-chr12:51417005..51419912,3	K562	blood:

Variant related genes	Relation type
SLC11A2	TF binding region
ENSG00000050426	Chromatin interaction
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10275	0.86[EUR][1000 genomes]
rs10783409	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876127	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876128	0.87[EUR][1000 genomes]
rs10876129	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876130	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10876131	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10876132	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876136	0.83[EUR][1000 genomes]
rs10876139	0.81[EUR][1000 genomes]
rs1095999	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169657	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169695	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12370120	0.80[EUR][1000 genomes]
rs12379	0.84[ASN][1000 genomes]
rs12424509	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12427345	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1486014	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs149411	0.80[EUR][1000 genomes]
rs15756	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1632791	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125111	0.96[ASN][1000 genomes]
rs2029145	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2029146	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs224572	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2554863	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2630370	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2630371	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs370462	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759405	0.84[ASN][1000 genomes]
rs427020	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4438107	0.81[EUR][1000 genomes]
rs4768947	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55874804	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61934800	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580782	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580785	0.83[EUR][1000 genomes]
rs706805	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135399	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7136960	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7969803	0.81[EUR][1000 genomes]
rs7971308	0.84[ASN][1000 genomes]
rs7976431	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7977740	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829015	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs829025	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9739342	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[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
rs224448	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	chr12:51378600-51393200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:51378600-51399000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:51378800-51396000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:51379400-51396000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:51379400-51396200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:51379600-51395600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:51379800-51394600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:51379800-51396400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:51380000-51396200	Strong transcription	Dnd41	blood
11	chr12:51380200-51391400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr12:51380200-51396400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:51380200-51396600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:51380200-51401800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr12:51380200-51402200	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr12:51380400-51391400	Strong transcription	Brain Germinal Matrix	brain
17	chr12:51380400-51396200	Strong transcription	Fetal Brain Female	brain
18	chr12:51380400-51396200	Strong transcription	Placenta	Placenta
19	chr12:51380600-51399600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:51380800-51391600	Strong transcription	Left Ventricle	heart
21	chr12:51381200-51391400	Strong transcription	Colon Smooth Muscle	Colon
22	chr12:51381200-51392200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr12:51381200-51395800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr12:51381200-51402200	Strong transcription	Fetal Thymus	thymus
25	chr12:51381200-51402200	Weak transcription	Psoas Muscle	Psoas
26	chr12:51381200-51402400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:51381200-51403000	Strong transcription	Fetal Muscle Leg	muscle
28	chr12:51381400-51394200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr12:51381400-51396400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:51381400-51403000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr12:51381800-51391400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr12:51381800-51391600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:51381800-51401600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:51381800-51401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:51381800-51402400	Strong transcription	Liver	Liver
36	chr12:51382000-51391400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:51382000-51391600	Strong transcription	Thymus	Thymus
38	chr12:51382000-51394600	Strong transcription	Lung	lung
39	chr12:51382000-51395800	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:51382000-51396400	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:51382000-51402000	Strong transcription	Fetal Stomach	stomach
42	chr12:51382000-51402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:51382400-51399400	Strong transcription	Fetal Intestine Large	intestine
44	chr12:51382600-51399400	Strong transcription	Fetal Intestine Small	intestine
45	chr12:51382800-51391400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:51383000-51393000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:51383800-51391400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:51384000-51394600	Strong transcription	HepG2	liver
49	chr12:51384400-51391800	Strong transcription	Brain Angular Gyrus	brain
50	chr12:51385600-51402600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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