Variant report

Variant	rs1720827
Chromosome Location	chr3:138126481-138126482
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138124875..138126534-chr3:138133315..138135134,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1199328	0.89[ASN][1000 genomes]
rs1199333	0.96[GIH][hapmap]
rs1199334	0.96[GIH][hapmap]
rs1199335	0.96[GIH][hapmap]
rs1201763	1.00[ASW][hapmap];0.86[CEU][hapmap];0.96[GIH][hapmap];0.90[TSI][hapmap]
rs1209710	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082471	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1308362	1.00[ASW][hapmap];0.96[GIH][hapmap]
rs1720825	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs253662	0.96[GIH][hapmap]
rs253664	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap]
rs253666	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40005	0.86[CEU][hapmap];0.96[GIH][hapmap];0.87[TSI][hapmap]
rs42761	1.00[ASW][hapmap];0.86[CEU][hapmap];0.96[GIH][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs4346503	1.00[ASN][1000 genomes]
rs4437085	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs808934	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
6	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
7	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1720827	A4GNT	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138109800-138131400	Weak transcription	NHDF-Ad	bronchial
2	chr3:138116000-138127000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:138117400-138126800	Weak transcription	Fetal Brain Male	brain
4	chr3:138118000-138127000	Weak transcription	Fetal Kidney	kidney
5	chr3:138118000-138131800	Weak transcription	Right Atrium	heart
6	chr3:138119400-138127000	Weak transcription	Psoas Muscle	Psoas
7	chr3:138120200-138126800	Weak transcription	HepG2	liver
8	chr3:138121400-138127000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:138121800-138126600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:138122200-138126800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:138123200-138127000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:138123400-138127200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:138123400-138127800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:138123800-138126800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:138123800-138128800	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:138123800-138129200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:138123800-138129600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:138123800-138131400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:138124000-138127000	Weak transcription	Brain Substantia Nigra	brain
20	chr3:138124000-138127200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:138124000-138127400	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:138124000-138129200	Weak transcription	Gastric	stomach
23	chr3:138124000-138131600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:138124000-138131800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:138124200-138126600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:138124400-138126600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:138124600-138126800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:138124600-138127400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:138124600-138129600	Weak transcription	Lung	lung
30	chr3:138124600-138131800	Weak transcription	Spleen	Spleen
31	chr3:138124600-138136000	Weak transcription	Adipose Nuclei	Adipose
32	chr3:138124800-138127200	Weak transcription	Brain Anterior Caudate	brain
33	chr3:138124800-138127400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:138124800-138127600	Weak transcription	Osteobl	bone
35	chr3:138124800-138130600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:138124800-138131600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:138124800-138131800	Weak transcription	Right Ventricle	heart
38	chr3:138124800-138132200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:138124800-138133000	Weak transcription	Left Ventricle	heart
40	chr3:138125000-138127400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:138125000-138127600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:138125000-138131400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:138125000-138131800	Weak transcription	Fetal Muscle Leg	muscle
44	chr3:138125200-138126600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:138125200-138127200	Weak transcription	Brain Germinal Matrix	brain
46	chr3:138125200-138127600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:138125200-138127600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:138125200-138127600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr3:138125200-138131400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:138125200-138131600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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