Variant report

Variant	rs1199333
Chromosome Location	chr3:138091701-138091702
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138089900..138093622-chr3:138093776..138096723,3	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1199328	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1199334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199335	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1199336	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199346	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1199347	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1201763	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1209710	0.96[GIH][hapmap];0.85[LWK][hapmap];0.87[AMR][1000 genomes]
rs1212469	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13082471	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1308362	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1624314	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166196	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679149	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1720825	0.89[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs183151	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs194146	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs253662	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253664	0.89[CEU][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap]
rs253666	0.82[YRI][hapmap];0.87[AMR][1000 genomes]
rs40005	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs40412	1.00[ASN][1000 genomes]
rs42761	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4346503	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4437085	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4678416	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6809480	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs774373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799328	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs811332	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv528349	chr3:138025396-138132393	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1796956	chr3:138051423-138122781	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1848610	chr3:138051423-138133412	Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv1797142	chr3:138087467-138122781	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1845560	chr3:138087467-138133412	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Amyotrophic lateral sclerosis (sporadic)	24529757	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1199333	A4GNT	cis	parietal	SCAN
rs1199333	LOC126536	trans	parietal	SCAN
rs1199333	SR140	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138068800-138093200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:138070000-138096600	Weak transcription	Fetal Brain Male	brain
3	chr3:138071200-138096600	Weak transcription	Aorta	Aorta
4	chr3:138074200-138095600	Enhancers	Fetal Heart	heart
5	chr3:138076000-138108200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:138078600-138100600	Weak transcription	NH-A	brain
7	chr3:138079600-138095600	Weak transcription	Fetal Brain Female	brain
8	chr3:138080200-138096400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:138080600-138092000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:138081600-138108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:138083000-138100400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:138083200-138091800	Enhancers	Adipose Nuclei	Adipose
13	chr3:138083200-138091800	Enhancers	Left Ventricle	heart
14	chr3:138083200-138100600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:138085200-138100000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:138085800-138096200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:138086200-138100400	Weak transcription	HepG2	liver
18	chr3:138086600-138091800	Weak transcription	Fetal Stomach	stomach
19	chr3:138086800-138100600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:138087000-138092000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:138087000-138096000	Weak transcription	Placenta	Placenta
22	chr3:138087200-138091800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:138087200-138092000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:138087200-138093400	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:138087200-138093400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:138087200-138097000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:138087200-138100000	Weak transcription	Pancreas	Pancrea
28	chr3:138087200-138100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:138087400-138097000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:138087600-138095000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:138087800-138092200	Enhancers	Right Atrium	heart
32	chr3:138088400-138093800	Weak transcription	Psoas Muscle	Psoas
33	chr3:138088800-138091800	Weak transcription	Osteobl	bone
34	chr3:138088800-138092000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:138089000-138091800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:138089200-138096200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:138089200-138100000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:138089200-138100800	Weak transcription	Fetal Lung	lung
39	chr3:138089400-138091800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:138089400-138091800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:138089400-138100000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:138089400-138100000	Weak transcription	Brain Angular Gyrus	brain
43	chr3:138089400-138102400	Weak transcription	Spleen	Spleen
44	chr3:138089600-138097600	Weak transcription	Brain Substantia Nigra	brain
45	chr3:138089600-138100200	Weak transcription	Lung	lung
46	chr3:138090000-138095200	Weak transcription	Brain Germinal Matrix	brain
47	chr3:138090200-138093400	Strong transcription	HSMMtube	muscle
48	chr3:138090400-138119400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:138090800-138091800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:138090800-138091800	Weak transcription	HSMM	muscle

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