Variant report

Variant	rs324019
Chromosome Location	chr12:57486647-57486648
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57484699-57487027	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:57486501-57489686	HL-60	blood:	n/a	n/a
3	POLR2A	chr12:57486122-57486879	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr12:57484187-57491110	K562	blood:	n/a	n/a
5	POLR2A	chr12:57486040-57491104	GM12878	blood:	n/a	n/a
6	STAT5A	chr12:57486640-57489743	GM12878	blood:	n/a	chr12:57488205-57488217 chr12:57488080-57488092 chr12:57488073-57488085 chr12:57487918-57487930
7	POLR2A	chr12:57485883-57487010	GM12892	blood:	n/a	n/a
8	POLR2A	chr12:57485487-57487906	A549	lung:	n/a	n/a
9	POLR2A	chr12:57486037-57490365	GM19193	blood:	n/a	n/a
10	SMC3	chr12:57486588-57486788	GM12878	blood:	n/a	n/a
11	POLR2A	chr12:57485551-57490658	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr12:57482691-57491598	SK-N-MC	brain:	n/a	n/a
13	MAZ	chr12:57486533-57489097	IMR90	lung:	n/a	chr12:57487133-57487143 chr12:57487909-57487919 chr12:57487789-57487799 chr12:57487012-57487022
14	POLR2A	chr12:57486630-57486688	MCF-7	breast:	n/a	n/a
15	POLR2A	chr12:57486039-57486689	GM12878	blood:	n/a	n/a
16	SMC3	chr12:57486506-57487543	SK-N-SH	brain:	n/a	chr12:57487053-57487063
17	POLR2A	chr12:57486360-57486743	Hela-S3	cervix:	n/a	n/a
18	MTA3	chr12:57486031-57490314	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:57485869-57491519	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:57485578-57491187	K562	blood:	n/a	n/a
21	POLR2A	chr12:57486588-57486993	GM12891	blood:	n/a	n/a
22	POLR2A	chr12:57486011-57486729	GM12892	blood:	n/a	n/a
23	POLR2A	chr12:57485689-57490808	GM12878	blood:	n/a	n/a
24	CTCF	chr12:57486231-57487616	A549	lung:	n/a	n/a
25	POLR2A	chr12:57484185-57491534	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57117928..57119916-chr12:57484796..57487169,2	K562	blood:
2	chr12:57486590..57487295-chr12:57576556..57577071,2	MCF-7	breast:
3	chr12:57393282..57404587-chr12:57480276..57487045,17	MCF-7	breast:

Variant related genes	Relation type
TMEM194A	TF binding region
ENSG00000166860	Chromatin interaction
ENSG00000196531	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs324010	0.87[GIH][hapmap];0.80[JPT][hapmap]
rs324018	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs841718	0.86[CHB][hapmap];0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs324019	STAT6	Cis_1M	lymphoblastoid	RTeQTL
rs324019	STAT6	cis	lymphoblastoid	seeQTL
rs324019	ACVR1B	cis	parietal	SCAN
rs324019	KRT75	cis	cerebellum	SCAN
rs324019	STAT6	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57483800-57492000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:57484000-57487200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:57484000-57487400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:57484000-57487400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr12:57484000-57498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:57484200-57486800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:57484200-57488400	Genic enhancers	Spleen	Spleen
8	chr12:57484400-57487800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
9	chr12:57484400-57487800	Transcr. at gene 5' and 3'	NHLF	lung
10	chr12:57484400-57490800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:57484400-57491000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:57484600-57487000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr12:57484600-57487200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:57484600-57488800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:57484600-57488800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:57484600-57489000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:57484800-57486800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
18	chr12:57484800-57487000	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr12:57484800-57487200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:57484800-57487200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:57484800-57487200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:57484800-57487400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:57484800-57487400	Genic enhancers	Primary T cells fromperipheralblood	blood
24	chr12:57484800-57487600	Weak transcription	Small Intestine	intestine
25	chr12:57484800-57487600	Genic enhancers	K562	blood
26	chr12:57484800-57488400	Genic enhancers	Fetal Lung	lung
27	chr12:57484800-57488400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
28	chr12:57484800-57488600	Genic enhancers	Right Ventricle	heart
29	chr12:57484800-57488800	Genic enhancers	Placenta	Placenta
30	chr12:57484800-57489000	Genic enhancers	Placenta Amnion	Placenta Amnion
31	chr12:57484800-57489400	Genic enhancers	Primary T cells from cord blood	blood
32	chr12:57484800-57490800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:57485000-57486800	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr12:57485000-57486800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:57485000-57486800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:57485000-57486800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:57485000-57487000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:57485000-57487000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:57485000-57487200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:57485000-57487200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:57485000-57487200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:57485000-57487400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:57485000-57487400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:57485000-57487400	Weak transcription	HUVEC	blood vessel
45	chr12:57485000-57487600	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:57485000-57488600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr12:57485000-57489000	Genic enhancers	Liver	Liver
48	chr12:57485000-57489400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:57485000-57490800	Genic enhancers	Fetal Thymus	thymus
50	chr12:57485000-57491000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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