Variant report

Variant	rs6580785
Chromosome Location	chr12:51483883-51483884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51479655..51481942-chr12:51483772..51485715,3	MCF-7	breast:
2	chr12:51475857..51479222-chr12:51481896..51486349,6	K562	blood:
3	chr12:51483401..51485613-chr12:51487391..51490176,3	K562	blood:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10275	0.95[EUR][1000 genomes]
rs10783409	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10783413	0.91[ASN][1000 genomes]
rs10876127	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876128	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs10876129	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876130	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10876131	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10876132	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10876136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876138	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs10876139	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169657	0.83[EUR][1000 genomes]
rs11169695	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11169707	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610644	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370120	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12379	1.00[CHB][hapmap]
rs12424509	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12427345	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1466579	0.89[ASN][1000 genomes]
rs1486014	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs15756	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1632791	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes]
rs17125111	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs17125340	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2029145	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2029146	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs224448	0.83[EUR][1000 genomes]
rs224572	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs224575	0.81[CEU][hapmap]
rs2730655	0.94[ASN][1000 genomes]
rs319936	0.81[CEU][hapmap]
rs319939	0.81[CEU][hapmap]
rs370462	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3759405	1.00[CHB][hapmap]
rs427020	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4438107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55874804	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61934800	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6580782	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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs6580791	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs706805	0.82[EUR][1000 genomes]
rs7135399	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7136960	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7953867	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs7958068	0.95[EUR][1000 genomes]
rs7961626	0.82[EUR][1000 genomes]
rs7969803	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971308	1.00[CHB][hapmap]
rs7976431	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7977740	0.81[EUR][1000 genomes]
rs901313	0.89[ASN][1000 genomes]
rs9739342	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[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
rs6580785	LETMD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477400-51488200	Weak transcription	Spleen	Spleen
2	chr12:51477400-51488800	Weak transcription	Gastric	stomach
3	chr12:51477400-51490000	Weak transcription	Small Intestine	intestine
4	chr12:51477400-51518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:51477600-51487800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:51477800-51484000	Weak transcription	HSMM	muscle
7	chr12:51477800-51484000	Weak transcription	HSMMtube	muscle
8	chr12:51477800-51484800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:51477800-51484800	Weak transcription	Brain Anterior Caudate	brain
10	chr12:51477800-51484800	Weak transcription	Fetal Lung	lung
11	chr12:51477800-51484800	Weak transcription	Osteobl	bone
12	chr12:51477800-51485000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:51477800-51485000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:51477800-51485000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:51477800-51485200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:51477800-51485400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:51477800-51485800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:51477800-51485800	Weak transcription	A549	lung
19	chr12:51477800-51486000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:51477800-51486000	Weak transcription	Lung	lung
21	chr12:51477800-51486800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:51477800-51487000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:51477800-51487000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:51477800-51487000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:51477800-51487000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:51477800-51487200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:51477800-51487200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:51477800-51487400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:51477800-51487400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:51477800-51487400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:51477800-51487400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr12:51477800-51487400	Weak transcription	HMEC	breast
33	chr12:51477800-51487600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:51477800-51487600	Weak transcription	Primary T cells from cord blood	blood
35	chr12:51477800-51487600	Weak transcription	Adipose Nuclei	Adipose
36	chr12:51477800-51487600	Weak transcription	Brain Substantia Nigra	brain
37	chr12:51477800-51487600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr12:51477800-51487800	Weak transcription	Liver	Liver
39	chr12:51477800-51487800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr12:51477800-51487800	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:51477800-51487800	Weak transcription	Left Ventricle	heart
42	chr12:51477800-51487800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:51477800-51487800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:51477800-51487800	Weak transcription	Hela-S3	cervix
45	chr12:51477800-51487800	Weak transcription	NH-A	brain
46	chr12:51477800-51487800	Weak transcription	NHDF-Ad	bronchial
47	chr12:51477800-51488000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:51477800-51488000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:51477800-51488000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr12:51477800-51488000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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