Variant report

Variant	rs329948
Chromosome Location	chr19:53031533-53031534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:53029127..53032188-chr19:53072538..53075129,3	K562	blood:
2	chr19:53029450..53032188-chr19:53072538..53074123,2	K562	blood:
3	chr19:53029459..53032258-chr19:53036873..53039549,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198482	Chromatin interaction
ENSG00000167562	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11882311	1.00[CHB][hapmap]
rs12461522	1.00[ASN][1000 genomes]
rs12462080	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12971372	1.00[ASN][1000 genomes]
rs12977988	1.00[ASN][1000 genomes]
rs12985487	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12986137	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16983943	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061355	1.00[ASN][1000 genomes]
rs28570374	1.00[ASN][1000 genomes]
rs329949	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34106830	1.00[ASN][1000 genomes]
rs34203482	1.00[ASN][1000 genomes]
rs34316627	1.00[ASN][1000 genomes]
rs34529833	1.00[ASN][1000 genomes]
rs34724169	1.00[ASN][1000 genomes]
rs34747259	1.00[ASN][1000 genomes]
rs34942135	1.00[ASN][1000 genomes]
rs35356792	1.00[ASN][1000 genomes]
rs35591322	1.00[ASN][1000 genomes]
rs35888888	1.00[ASN][1000 genomes]
rs35895760	1.00[ASN][1000 genomes]
rs35904532	1.00[ASN][1000 genomes]
rs36089907	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382838	1.00[ASN][1000 genomes]
rs436426	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4401146	1.00[CHB][hapmap]
rs557496	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58067500	1.00[ASN][1000 genomes]
rs71358875	1.00[ASN][1000 genomes]
rs71358876	1.00[ASN][1000 genomes]
rs71358877	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71358878	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71358879	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71358884	1.00[ASN][1000 genomes]
rs7252479	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257799	0.83[EUR][1000 genomes]
rs7257824	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73578236	1.00[ASN][1000 genomes]
rs73578252	1.00[ASN][1000 genomes]
rs8104197	1.00[ASN][1000 genomes]
rs811920	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3404701	chr19:52986895-53035152	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3440535	chr19:52993529-53035203	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1064342	chr19:52996710-53041119	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1055825	chr19:53001299-53037378	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1055859	chr19:53001299-53041119	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1060656	chr19:53001299-53041995	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs329948	UGT2A3	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53029600-53032000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr19:53029600-53032000	Active TSS	HSMM	muscle
3	chr19:53029600-53032200	Active TSS	Colonic Mucosa	Colon
4	chr19:53030000-53031600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:53030000-53031600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:53030000-53031600	Active TSS	Brain Anterior Caudate	brain
7	chr19:53030000-53031600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:53030000-53031600	Active TSS	Colon Smooth Muscle	Colon
9	chr19:53030000-53031600	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr19:53030000-53031600	Active TSS	NHLF	lung
11	chr19:53030000-53031600	Active TSS	Osteobl	bone
12	chr19:53030000-53031800	Active TSS	H1 Cell Line	embryonic stem cell
13	chr19:53030000-53031800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:53030000-53031800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:53030000-53031800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:53030000-53031800	Active TSS	Fetal Kidney	kidney
17	chr19:53030000-53031800	Active TSS	Right Atrium	heart
18	chr19:53030000-53032000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:53030000-53032000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:53030000-53032000	Active TSS	Fetal Intestine Small	intestine
21	chr19:53030000-53032000	Active TSS	HMEC	breast
22	chr19:53030000-53032200	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr19:53030000-53032400	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr19:53030000-53032400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:53030000-53032600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:53030200-53031600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:53030200-53031600	Active TSS	Brain Substantia Nigra	brain
28	chr19:53030200-53031600	Active TSS	Fetal Lung	lung
29	chr19:53030200-53031600	Active TSS	Gastric	stomach
30	chr19:53030200-53031600	Active TSS	NHEK	skin
31	chr19:53030200-53031800	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr19:53030200-53031800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr19:53030200-53031800	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr19:53030200-53031800	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr19:53030200-53031800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:53030200-53031800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:53030200-53031800	Active TSS	Aorta	Aorta
38	chr19:53030200-53031800	Active TSS	Brain Angular Gyrus	brain
39	chr19:53030200-53031800	Active TSS	Esophagus	oesophagus
40	chr19:53030200-53031800	Active TSS	Left Ventricle	heart
41	chr19:53030200-53031800	Active TSS	Ovary	ovary
42	chr19:53030200-53031800	Active TSS	NHDF-Ad	bronchial
43	chr19:53030200-53032000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr19:53030200-53032000	Active TSS	Muscle Satellite Cultured Cells	--
45	chr19:53030200-53032000	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr19:53030200-53032000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr19:53030200-53032000	Active TSS	NH-A	brain
48	chr19:53030200-53032200	Active TSS	Hela-S3	cervix
49	chr19:53030200-53032600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr19:53030400-53031600	Active TSS	Fetal Heart	heart

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