Variant report

Variant	rs7138945
Chromosome Location	chr12:50539419-50539420
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50535984..50537611-chr12:50539393..50542341,2	K562	blood:
2	chr12:50529914..50531795-chr12:50537950..50540041,2	K562	blood:
3	chr12:50531935..50534070-chr12:50539130..50540855,2	K562	blood:
4	chr12:50478449..50481902-chr12:50536030..50539935,3	MCF-7	breast:
5	chr12:50497375..50499657-chr12:50539250..50540993,2	K562	blood:

Variant related genes	Relation type
ENSG00000066117	Chromatin interaction
ENSG00000167588	Chromatin interaction
ENSG00000139624	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10735824	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783338	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10876000	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169278	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169281	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169282	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12369049	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12369104	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12819883	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1554844	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1554845	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17124432	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2204683	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3184122	0.80[CEU][hapmap];0.84[GIH][hapmap]
rs34167640	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3741562	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59262224	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6580728	0.96[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66782120	0.87[ASN][1000 genomes]
rs7135322	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7138420	0.84[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap]
rs7138622	0.81[YRI][hapmap]
rs7294618	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7307230	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7307469	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7308474	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7315690	0.84[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap]
rs7398567	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7961065	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7961112	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7964698	0.85[EUR][1000 genomes]
rs7967979	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7968119	0.96[CEU][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7972465	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7978904	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9364	0.85[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7138945	CERS5	cis	Muscle Skeletal	GTEx
rs7138945	LASS5	cis	cerebellum	SCAN
rs7138945	CERS5	cis	Nerve Tibial	GTEx
rs7138945	LASS5	cis	parietal	SCAN
rs7138945	RPAP3	cis	cerebellum	SCAN
rs7138945	SLC38A1	cis	parietal	SCAN
rs7138945	SNORA2A	cis	parietal	SCAN
rs7138945	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs7138945	ATF1	cis	parietal	SCAN
rs7138945	KIAA1463	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
2	chr12:50517600-50548000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:50524000-50559800	Weak transcription	Right Atrium	heart
4	chr12:50524600-50541600	Weak transcription	Psoas Muscle	Psoas
5	chr12:50528800-50543000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:50529600-50542800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:50529800-50543000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:50529800-50559800	Weak transcription	NHLF	lung
9	chr12:50530000-50539600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:50530000-50559600	Weak transcription	A549	lung
11	chr12:50530000-50560200	Weak transcription	Esophagus	oesophagus
12	chr12:50531200-50548400	Weak transcription	HUVEC	blood vessel
13	chr12:50531600-50543200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:50531600-50558200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:50531800-50544600	Weak transcription	Fetal Kidney	kidney
16	chr12:50531800-50554400	Weak transcription	K562	blood
17	chr12:50531800-50558400	Weak transcription	Fetal Brain Male	brain
18	chr12:50532000-50539600	Weak transcription	Brain Substantia Nigra	brain
19	chr12:50532000-50560200	Weak transcription	Aorta	Aorta
20	chr12:50532000-50560200	Weak transcription	Gastric	stomach
21	chr12:50532400-50541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:50532400-50541400	Weak transcription	Liver	Liver
23	chr12:50532400-50559800	Weak transcription	Spleen	Spleen
24	chr12:50532800-50542200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:50533200-50544800	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:50533200-50559400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr12:50533400-50551200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:50534400-50560200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:50534600-50544800	Weak transcription	Ovary	ovary
30	chr12:50535000-50545400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:50535200-50541800	Weak transcription	Lung	lung
32	chr12:50535200-50545000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:50535200-50560000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:50535200-50560200	Weak transcription	Right Ventricle	heart
35	chr12:50535400-50559400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr12:50535400-50560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:50536400-50560200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr12:50536800-50545000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr12:50537000-50539800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr12:50537000-50544600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:50537200-50539600	Weak transcription	Fetal Intestine Large	intestine
42	chr12:50537200-50558200	Weak transcription	Fetal Brain Female	brain
43	chr12:50537200-50559200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr12:50537400-50543000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr12:50537400-50550600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:50537400-50559400	Weak transcription	Brain Hippocampus Middle	brain
47	chr12:50537400-50560200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:50537600-50559400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr12:50537600-50559400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr12:50537800-50539600	Weak transcription	Adipose Nuclei	Adipose

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