Variant report

Variant	rs6580782
Chromosome Location	chr12:51443469-51443470
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51421719..51422616-chr12:51442889..51443788,2	MCF-7	breast:
2	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
3	chr12:51440588..51444188-chr12:51475693..51478745,10	K562	blood:
4	chr12:51440271..51447226-chr12:51475135..51479930,16	MCF-7	breast:
5	chr12:51418602..51423346-chr12:51439309..51444851,15	MCF-7	breast:
6	chr12:51439067..51445190-chr12:51449547..51456560,11	K562	blood:
7	chr12:51421116..51422954-chr12:51442627..51444321,2	K562	blood:
8	chr12:51157036..51159803-chr12:51442013..51443781,2	K562	blood:
9	chr12:51440642..51443592-chr12:51616961..51619958,3	MCF-7	breast:
10	chr12:51156477..51159239-chr12:51440349..51444629,5	K562	blood:
11	chr12:51440743..51444863-chr12:51448295..51453075,7	MCF-7	breast:
12	chr12:51440639..51443821-chr12:51630707..51634068,3	K562	blood:
13	chr12:51399373..51401239-chr12:51441069..51443548,3	MCF-7	breast:
14	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
15	chr12:51441811..51444855-chr12:51447426..51450145,3	K562	blood:
16	chr12:51440782..51445752-chr12:51631445..51635429,5	MCF-7	breast:
17	chr12:51442131..51443654-chr12:51632359..51634023,2	MCF-7	breast:
18	chr12:51441619..51444815-chr12:51631402..51636504,5	K562	blood:
19	chr12:51440588..51444188-chr12:51475774..51478819,7	K562	blood:
20	chr12:51440852..51445521-chr12:51475730..51478507,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000269339	Chromatin interaction
ENSG00000050426	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10275	0.98[EUR][1000 genomes]
rs10783409	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10876127	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876128	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10876129	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876130	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876132	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876136	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10876138	1.00[CHB][hapmap]
rs10876139	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1095999	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169657	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169695	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169707	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11169710	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11610644	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12370120	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12379	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs12424509	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12427345	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1486014	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1632791	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17125111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17125340	0.82[CHB][hapmap]
rs2010630	0.86[ASN][1000 genomes]
rs2029145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224448	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs224572	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs224575	0.84[CEU][hapmap]
rs2554863	0.88[ASN][1000 genomes]
rs2630371	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs319936	0.84[CEU][hapmap]
rs319939	0.84[CEU][hapmap]
rs370462	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759405	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs427020	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4438107	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4768947	0.88[ASN][1000 genomes]
rs55874804	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61934800	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580785	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6580788	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6580791	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs706805	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7135399	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136960	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953867	1.00[CHB][hapmap]
rs7958068	0.91[EUR][1000 genomes]
rs7961626	0.86[EUR][1000 genomes]
rs7969803	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7971308	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7976431	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977740	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs829025	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9739342	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs6580782	LETMD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51441000-51443600	Active TSS	Psoas Muscle	Psoas
2	chr12:51442200-51443600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:51442200-51443600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
4	chr12:51442400-51443600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr12:51442400-51443600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:51442400-51443600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr12:51442400-51443600	Flanking Active TSS	Rectal Smooth Muscle	rectum
8	chr12:51442400-51443600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr12:51442600-51443600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:51442600-51443600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr12:51442600-51443600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr12:51442600-51443600	Flanking Active TSS	Fetal Heart	heart
13	chr12:51442600-51443600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr12:51442600-51443600	Flanking Active TSS	Fetal Lung	lung
15	chr12:51442600-51443600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr12:51442600-51443600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr12:51442600-51443600	Flanking Active TSS	NH-A	brain
18	chr12:51442600-51443600	Flanking Active TSS	NHDF-Ad	bronchial
19	chr12:51442600-51443600	Flanking Active TSS	NHLF	lung
20	chr12:51442600-51443800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:51442600-51443800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:51442600-51443800	Flanking Active TSS	Hela-S3	cervix
23	chr12:51442600-51443800	Flanking Active TSS	HUVEC	blood vessel
24	chr12:51442600-51443800	Flanking Active TSS	NHEK	skin
25	chr12:51442800-51443600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr12:51442800-51443600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:51442800-51443600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr12:51442800-51443600	Flanking Active TSS	HMEC	breast
29	chr12:51442800-51443800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:51442800-51444000	Flanking Active TSS	Dnd41	blood
31	chr12:51442800-51448200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:51442800-51449000	Weak transcription	Aorta	Aorta
33	chr12:51442800-51449800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:51442800-51450000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:51442800-51452800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:51442800-51470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr12:51443000-51443600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:51443000-51443600	Enhancers	Primary B cells from cord blood	blood
39	chr12:51443000-51443600	Enhancers	Primary B cells from peripheral blood	blood
40	chr12:51443000-51443600	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr12:51443000-51443600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:51443000-51443600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:51443000-51443600	Enhancers	Fetal Muscle Leg	muscle
44	chr12:51443000-51443600	Enhancers	Fetal Thymus	thymus
45	chr12:51443000-51443600	Enhancers	Small Intestine	intestine
46	chr12:51443000-51443600	Enhancers	Thymus	Thymus
47	chr12:51443000-51443800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr12:51443000-51443800	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr12:51443000-51444400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr12:51443000-51445400	Weak transcription	Left Ventricle	heart

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