Variant report

Variant	rs324020
Chromosome Location	chr12:57486033-57486034
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57485889-57486560	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:57484699-57487027	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr12:57485881-57486551	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:57484187-57491110	K562	blood:	n/a	n/a
5	POLR2A	chr12:57485944-57486592	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:57485883-57487010	GM12892	blood:	n/a	n/a
7	POLR2A	chr12:57485487-57487906	A549	lung:	n/a	n/a
8	STAT5A	chr12:57486016-57486298	GM12878	blood:	n/a	n/a
9	TEAD4	chr12:57485887-57486511	K562	blood:	n/a	n/a
10	POLR2A	chr12:57485551-57490658	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr12:57482691-57491598	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr12:57485976-57486355	MCF-7	breast:	n/a	n/a
13	POLR2A	chr12:57485853-57486110	HCT-116	colon:	n/a	n/a
14	MTA3	chr12:57486031-57490314	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:57485869-57491519	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:57485578-57491187	K562	blood:	n/a	n/a
17	POLR2A	chr12:57486011-57486729	GM12892	blood:	n/a	n/a
18	POLR2A	chr12:57485897-57486130	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr12:57485689-57490808	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:57484185-57491534	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57483952..57486497-chr12:57580881..57583064,2	K562	blood:
2	chr12:57117928..57119916-chr12:57484796..57487169,2	K562	blood:
3	chr12:57393282..57404587-chr12:57480276..57487045,17	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM194A	TF binding region
ENSG00000123384	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000166860	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1044931	0.96[CEU][hapmap]
rs167769	1.00[JPT][hapmap]
rs324010	0.89[CEU][hapmap]
rs324011	1.00[JPT][hapmap]
rs324021	0.96[CEU][hapmap]
rs703817	1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs841718	0.82[JPT][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57483800-57486600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:57483800-57492000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:57484000-57487200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:57484000-57487400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:57484000-57487400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr12:57484000-57498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:57484200-57486800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:57484200-57488400	Genic enhancers	Spleen	Spleen
9	chr12:57484400-57486400	Genic enhancers	Dnd41	blood
10	chr12:57484400-57487800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
11	chr12:57484400-57487800	Transcr. at gene 5' and 3'	NHLF	lung
12	chr12:57484400-57490800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:57484400-57491000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:57484600-57487000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr12:57484600-57487200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:57484600-57488800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:57484600-57488800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:57484600-57489000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:57484800-57486200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr12:57484800-57486200	Enhancers	Fetal Brain Male	brain
21	chr12:57484800-57486200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr12:57484800-57486200	Weak transcription	Hela-S3	cervix
23	chr12:57484800-57486400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:57484800-57486600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr12:57484800-57486800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr12:57484800-57487000	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr12:57484800-57487200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:57484800-57487200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:57484800-57487200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:57484800-57487400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr12:57484800-57487400	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr12:57484800-57487600	Weak transcription	Small Intestine	intestine
33	chr12:57484800-57487600	Genic enhancers	K562	blood
34	chr12:57484800-57488400	Genic enhancers	Fetal Lung	lung
35	chr12:57484800-57488400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
36	chr12:57484800-57488600	Genic enhancers	Right Ventricle	heart
37	chr12:57484800-57488800	Genic enhancers	Placenta	Placenta
38	chr12:57484800-57489000	Genic enhancers	Placenta Amnion	Placenta Amnion
39	chr12:57484800-57489400	Genic enhancers	Primary T cells from cord blood	blood
40	chr12:57484800-57490800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:57485000-57486200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:57485000-57486200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:57485000-57486200	Genic enhancers	Esophagus	oesophagus
44	chr12:57485000-57486200	Weak transcription	Stomach Mucosa	stomach
45	chr12:57485000-57486400	Strong transcription	A549	lung
46	chr12:57485000-57486400	Genic enhancers	GM12878-XiMat	blood
47	chr12:57485000-57486600	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
48	chr12:57485000-57486800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr12:57485000-57486800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:57485000-57486800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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