Variant report

Variant	rs7972465
Chromosome Location	chr12:50546125-50546126
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50544718..50546779-chr12:50552801..50555276,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10735824	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783340	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169278	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169282	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12369049	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12369104	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12424335	0.80[EUR][1000 genomes]
rs12819883	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1554844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1554845	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17124432	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17124514	0.81[JPT][hapmap]
rs2204683	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3184122	0.84[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs34167640	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3741562	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59262224	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6580728	1.00[CEU][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7135322	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7138420	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs7138945	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]
rs7294618	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7307230	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7307469	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7308474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7315690	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs7398567	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7961065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7961112	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7964698	0.82[EUR][1000 genomes]
rs7967979	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7968119	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7978904	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9364	0.88[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]

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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7972465	KIAA1463	cis	multi-tissue	Pritchard
rs7972465	SLC38A1	cis	parietal	SCAN
rs7972465	SNORA2A	cis	parietal	SCAN
rs7972465	EPLIN	cis	multi-tissue	Pritchard
rs7972465	LASS5	cis	cerebellum	SCAN
rs7972465	CERS5	cis	Muscle Skeletal	GTEx
rs7972465	CERS5	cis	Nerve Tibial	GTEx
rs7972465	LASS5	cis	parietal	SCAN
rs7972465	LASS5	cis	multi-tissue	Pritchard
rs7972465	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs7972465	ATF1	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50517600-50548000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:50524000-50559800	Weak transcription	Right Atrium	heart
3	chr12:50529800-50559800	Weak transcription	NHLF	lung
4	chr12:50530000-50559600	Weak transcription	A549	lung
5	chr12:50530000-50560200	Weak transcription	Esophagus	oesophagus
6	chr12:50531200-50548400	Weak transcription	HUVEC	blood vessel
7	chr12:50531600-50558200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:50531800-50554400	Weak transcription	K562	blood
9	chr12:50531800-50558400	Weak transcription	Fetal Brain Male	brain
10	chr12:50532000-50560200	Weak transcription	Aorta	Aorta
11	chr12:50532000-50560200	Weak transcription	Gastric	stomach
12	chr12:50532400-50559800	Weak transcription	Spleen	Spleen
13	chr12:50533200-50559400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr12:50533400-50551200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:50534400-50560200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:50535200-50560000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:50535200-50560200	Weak transcription	Right Ventricle	heart
18	chr12:50535400-50559400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr12:50535400-50560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:50536400-50560200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:50537200-50558200	Weak transcription	Fetal Brain Female	brain
22	chr12:50537200-50559200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:50537400-50550600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:50537400-50559400	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:50537400-50560200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:50537600-50559400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr12:50537600-50559400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:50537800-50547400	Weak transcription	Primary T cells from cord blood	blood
29	chr12:50537800-50550400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:50537800-50551200	Weak transcription	HepG2	liver
31	chr12:50537800-50553600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr12:50537800-50554200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:50537800-50554400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:50537800-50554800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr12:50537800-50555800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:50537800-50556000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr12:50537800-50558200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:50537800-50558400	Weak transcription	Placenta	Placenta
39	chr12:50537800-50559200	Weak transcription	GM12878-XiMat	blood
40	chr12:50537800-50559400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:50537800-50559400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:50537800-50559400	Weak transcription	Fetal Lung	lung
43	chr12:50537800-50559800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:50537800-50559800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:50537800-50560200	Weak transcription	Left Ventricle	heart
46	chr12:50538000-50547400	Weak transcription	NHEK	skin
47	chr12:50538000-50554000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:50538000-50556000	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr12:50538200-50546400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:50538200-50547200	Weak transcription	Thymus	Thymus

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