Variant report

Variant	rs6580729
Chromosome Location	chr12:50547038-50547039
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1044370	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10747570	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10783342	0.90[ASW][hapmap];0.93[LWK][hapmap];0.91[YRI][hapmap]
rs11169294	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169300	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11831413	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12426261	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12815871	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12824125	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12830386	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2178173	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2358538	0.81[ASW][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs34573394	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35549836	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35998534	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4459386	0.81[ASW][hapmap]
rs4883481	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4883482	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56709084	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646782	1.00[CHB][hapmap]
rs6580738	0.82[LWK][hapmap]
rs66768395	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs706791	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs706792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs706793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7136570	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7279	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7294548	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297421	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7301566	0.83[ASN][1000 genomes]
rs7301649	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301740	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7302981	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7308356	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7957659	0.81[ASW][hapmap]
rs7967705	0.87[EUR][1000 genomes]
rs7967844	0.88[EUR][1000 genomes]
rs7967954	0.90[ASW][hapmap];0.87[LWK][hapmap];0.91[YRI][hapmap]
rs7972842	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8181679	0.90[ASW][hapmap];0.82[LWK][hapmap];0.91[YRI][hapmap]
rs836172	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs836177	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs836179	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836180	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs844347	0.84[GIH][hapmap]
rs860698	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6580729	LASS5	cis	parietal	SCAN
rs6580729	DIP2B	cis	cerebellum	SCAN
rs6580729	LASS5	cis	multi-tissue	Pritchard
rs6580729	MCRS1	cis	parietal	SCAN
rs6580729	SNORA2A	cis	parietal	SCAN
rs6580729	CERS5	cis	Nerve Tibial	GTEx
rs6580729	LASS5	cis	cerebellum	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	chr12:50538200-50547200	Weak transcription	Thymus	Thymus
50	chr12:50538200-50547400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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