Variant report

Variant	rs1044370
Chromosome Location	chr12:50570610-50570611
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50496386..50497971-chr12:50569174..50571228,2	MCF-7	breast:
2	chr12:50471994..50474538-chr12:50569711..50571544,2	MCF-7	breast:
3	chr12:50479656..50481335-chr12:50569381..50571958,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167588	Chromatin interaction
ENSG00000110881	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10783342	0.90[ASW][hapmap];0.93[LWK][hapmap];0.83[YRI][hapmap]
rs11169294	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11169300	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11831413	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12426261	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12815871	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12824125	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12830386	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1862043	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1979702	0.85[CEU][hapmap]
rs2178173	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2272391	0.88[CEU][hapmap]
rs2358538	0.81[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs34573394	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35549836	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35998534	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4459386	0.81[ASW][hapmap]
rs4883481	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4883482	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56709084	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs646782	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs6580729	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]
rs6580738	0.82[LWK][hapmap]
rs66768395	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs706791	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs706792	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs706793	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7136570	0.90[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs7279	0.90[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap]
rs7294548	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7297421	0.90[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap]
rs7301566	0.90[ASN][1000 genomes]
rs7301649	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7302981	0.90[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7308356	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7532	0.90[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap]
rs7957659	0.81[ASW][hapmap]
rs7967954	0.90[ASW][hapmap];0.87[LWK][hapmap];0.83[YRI][hapmap]
rs8181679	0.90[ASW][hapmap];0.82[LWK][hapmap];0.83[YRI][hapmap]
rs835592	0.88[CEU][hapmap]
rs836172	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs836177	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs836179	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs836180	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs844347	0.88[CEU][hapmap]
rs860698	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]

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	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
2	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1044370	LASS5	cis	parietal	SCAN
rs1044370	LASS5	cis	cerebellum	SCAN
rs1044370	LASS5	cis	multi-tissue	Pritchard
rs1044370	SNORA2A	cis	parietal	SCAN
rs1044370	CERS5	cis	Nerve Tibial	GTEx
rs1044370	RND1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50561600-50570800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:50561600-50570800	Weak transcription	Esophagus	oesophagus
3	chr12:50561600-50570800	Weak transcription	Gastric	stomach
4	chr12:50561600-50570800	Weak transcription	Pancreas	Pancrea
5	chr12:50561600-50571200	Weak transcription	Lung	lung
6	chr12:50561600-50571200	Weak transcription	Right Ventricle	heart
7	chr12:50561600-50575200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:50561800-50570800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:50561800-50570800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr12:50561800-50570800	Weak transcription	Brain Angular Gyrus	brain
11	chr12:50561800-50570800	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:50561800-50570800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr12:50561800-50570800	Weak transcription	Ovary	ovary
14	chr12:50561800-50571000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:50561800-50571000	Weak transcription	Colonic Mucosa	Colon
16	chr12:50561800-50571000	Weak transcription	Spleen	Spleen
17	chr12:50561800-50571200	Weak transcription	Brain Germinal Matrix	brain
18	chr12:50561800-50571200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:50561800-50571200	Weak transcription	Left Ventricle	heart
20	chr12:50561800-50571200	Weak transcription	Thymus	Thymus
21	chr12:50561800-50573000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:50561800-50574800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr12:50561800-50574800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:50561800-50575000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:50561800-50582600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr12:50561800-50582600	Weak transcription	Stomach Mucosa	stomach
27	chr12:50562000-50570800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:50562000-50571000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:50562000-50571000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:50562000-50571400	Weak transcription	Fetal Lung	lung
31	chr12:50562000-50576000	Weak transcription	Fetal Heart	heart
32	chr12:50562000-50576400	Weak transcription	A549	lung
33	chr12:50562000-50584800	Weak transcription	K562	blood
34	chr12:50562200-50597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:50564400-50570800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:50564400-50586200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr12:50564600-50571000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr12:50564600-50571200	Weak transcription	HepG2	liver
40	chr12:50566000-50570800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:50566200-50570800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:50566400-50571200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:50567800-50578800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:50568200-50578200	Strong transcription	Fetal Intestine Large	intestine
45	chr12:50568600-50577800	Strong transcription	NHDF-Ad	bronchial
46	chr12:50568600-50582000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr12:50568800-50581400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr12:50569000-50570800	Weak transcription	Fetal Stomach	stomach
49	chr12:50569000-50572600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr12:50569000-50572600	Strong transcription	HMEC	breast

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