Variant report

Variant	rs12072840
Chromosome Location	chr1:114353558-114353559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:32)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr1:114353147-114355793	SK-N-SH	brain:	n/a	n/a
2	EGR1	chr1:114353034-114356186	MCF-7	breast:	n/a	n/a
3	POLR2A	chr1:114353126-114355605	MCF10A-Er-Src	breast:	n/a	n/a
4	MAZ	chr1:114353484-114355777	IMR90	lung:	n/a	n/a
5	HCFC1	chr1:114353440-114355763	Hela-S3	cervix:	n/a	n/a
6	SIN3AK20	chr1:114353302-114355963	MCF-7	breast:	n/a	n/a
7	PML	chr1:114353501-114355672	MCF-7	breast:	n/a	n/a
8	MXI1	chr1:114353501-114355688	GM12878	blood:	n/a	n/a
9	EGR1	chr1:114353543-114355752	MCF-7	breast:	n/a	n/a
10	MXI1	chr1:114353169-114355409	Hela-S3	cervix:	n/a	n/a
11	ELF1	chr1:114353354-114355768	MCF-7	breast:	n/a	chr1:114353502-114353513
12	JUN	chr1:114352049-114356471	K562	blood:	n/a	n/a
13	TBP	chr1:114353550-114354416	Hela-S3	cervix:	n/a	n/a
14	TAF1	chr1:114353470-114355767	MCF-7	breast:	n/a	n/a

No data

(count:32 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114353442..114355343-chr17:57922180..57925150,2	MCF-7	breast:
2	chr1:114353355..114355590-chr17:57860876..57862433,2	MCF-7	breast:
3	chr1:114327966..114331682-chr1:114351317..114354646,4	K562	blood:
4	chr1:114324677..114327047-chr1:114352445..114354886,5	MCF-7	breast:
5	chr1:114351776..114354778-chr1:114417690..114420488,3	MCF-7	breast:
6	chr1:114352745..114355342-chr1:114397110..114401660,4	MCF-7	breast:
7	chr1:114351760..114356326-chr1:114471041..114474785,9	K562	blood:
8	chr1:114352914..114355173-chr8:67972851..67974547,2	MCF-7	breast:
9	chr1:114352160..114355349-chr1:114470537..114474785,4	K562	blood:
10	chr1:114353271..114354789-chr1:114442800..114445051,2	MCF-7	breast:
11	chr1:114353393..114356662-chr20:49346921..49350434,3	MCF-7	breast:
12	chr1:114352306..114358140-chr1:114445806..114450844,18	MCF-7	breast:
13	chr1:114299192..114304079-chr1:114351100..114353758,4	K562	blood:
14	chr1:108226178..108228590-chr1:114353094..114356101,3	MCF-7	breast:
15	chr1:108269564..108272129-chr1:114352003..114353705,2	MCF-7	breast:
16	chr1:114353074..114355128-chr9:133814434..133817147,2	MCF-7	breast:
17	chr1:114307008..114312126-chr1:114352475..114355930,7	MCF-7	breast:
18	chr1:108229330..108231475-chr1:114352461..114355425,3	MCF-7	breast:
19	chr1:114353249..114355008-chr17:59488182..59490622,2	MCF-7	breast:
20	chr1:114353086..114356383-chr1:114467552..114475359,15	MCF-7	breast:
21	chr1:114353164..114356409-chr1:114439569..114442509,4	MCF-7	breast:
22	chr1:114352137..114357235-chr1:114445065..114452395,18	MCF-7	breast:
23	chr1:114352766..114354968-chr1:114504894..114507135,2	MCF-7	breast:
24	chr1:114300040..114303354-chr1:114351974..114356702,9	MCF-7	breast:
25	chr1:114353223..114356831-chr1:115298921..115302043,5	MCF-7	breast:
26	chr1:114352743..114357488-chr1:114365626..114369516,6	MCF-7	breast:
27	chr1:114298167..114305255-chr1:114351008..114356451,27	MCF-7	breast:
28	chr1:114353109..114354990-chr1:114522325..114525289,2	MCF-7	breast:
29	chr1:108291627..108293246-chr1:114353081..114355950,2	MCF-7	breast:
30	chr1:114352067..114356642-chr1:114470131..114477025,16	MCF-7	breast:
31	chr1:114352670..114354884-chr1:114372315..114375244,2	K562	blood:
32	chr1:114351754..114354517-chr1:115321851..115324314,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231128	TF binding region
ENSG00000118655	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000226167	Chromatin interaction
ENSG00000121022	Chromatin interaction
ENSG00000267637	Chromatin interaction
ENSG00000134215	Chromatin interaction
ENSG00000116774	Chromatin interaction
ENSG00000052723	Chromatin interaction
ENSG00000130720	Chromatin interaction
ENSG00000009307	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000163349	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1039538	1.00[ASN][1000 genomes]
rs11102679	0.85[EUR][1000 genomes]
rs11102680	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12060671	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12063602	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12064048	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12086911	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12090627	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12094849	0.84[EUR][1000 genomes]
rs12095398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12097198	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1394074	1.00[ASN][1000 genomes]
rs34639107	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35061908	1.00[ASN][1000 genomes]
rs41274108	1.00[ASN][1000 genomes]
rs55946257	1.00[AMR][1000 genomes]
rs61013095	1.00[ASN][1000 genomes]
rs61324555	1.00[ASN][1000 genomes]
rs998315	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114303400-114353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:114320000-114354000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:114329200-114353600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:114348200-114353600	Weak transcription	Placenta	Placenta
5	chr1:114348600-114353800	Weak transcription	Gastric	stomach
6	chr1:114349800-114353600	Weak transcription	Lung	lung
7	chr1:114351000-114353600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:114351400-114354000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:114351600-114353600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:114351600-114353600	Enhancers	Fetal Heart	heart
11	chr1:114351600-114353800	Weak transcription	Pancreas	Pancrea
12	chr1:114351800-114353600	Enhancers	Primary B cells from peripheral blood	blood
13	chr1:114351800-114355400	Active TSS	NHLF	lung
14	chr1:114351800-114355600	Active TSS	Psoas Muscle	Psoas
15	chr1:114352000-114353600	Weak transcription	Stomach Mucosa	stomach
16	chr1:114352000-114353600	Active TSS	Stomach Smooth Muscle	stomach
17	chr1:114352000-114353800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:114352000-114354400	Active TSS	Right Atrium	heart
19	chr1:114352000-114355800	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr1:114352000-114355800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:114352200-114355400	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr1:114352200-114355400	Active TSS	GM12878-XiMat	blood
23	chr1:114352200-114355400	Active TSS	Hela-S3	cervix
24	chr1:114352200-114355800	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr1:114352400-114353600	Flanking Active TSS	HUVEC	blood vessel
26	chr1:114352400-114354200	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr1:114352400-114354200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:114352400-114354400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr1:114352400-114355200	Active TSS	Primary T cells fromperipheralblood	blood
30	chr1:114352400-114355400	Active TSS	Fetal Intestine Large	intestine
31	chr1:114352400-114355400	Active TSS	Fetal Thymus	thymus
32	chr1:114352400-114355800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:114352400-114356200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:114352600-114354000	Flanking Active TSS	Liver	Liver
35	chr1:114352600-114354200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:114352600-114354400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr1:114352600-114354400	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr1:114352600-114354600	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr1:114352600-114355400	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr1:114352600-114355400	Active TSS	HSMM	muscle
41	chr1:114352600-114355600	Active TSS	H1 Cell Line	embryonic stem cell
42	chr1:114352600-114355600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:114352600-114355800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:114352600-114355800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:114352600-114355800	Active TSS	A549	lung
46	chr1:114352600-114355800	Active TSS	HSMMtube	muscle
47	chr1:114352800-114353600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:114352800-114353600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:114352800-114354000	Weak transcription	Spleen	Spleen
50	chr1:114352800-114354000	Active TSS	HepG2	liver

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