Variant report

Variant	rs12440904
Chromosome Location	chr15:59158323-59158324
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:59156745-59158918	NB4	blood:	n/a	n/a
2	POLR2A	chr15:59156453-59158833	HepG2	liver:	n/a	n/a
3	TCF12	chr15:59158295-59158839	ECC-1	luminal epithelium:	n/a	n/a
4	SP1	chr15:59158309-59158847	A549	lung:	n/a	n/a
5	RPC155	chr15:59157933-59158663	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:59156716-59158766	HepG2	liver:	n/a	n/a
7	MYC	chr15:59156638-59158881	NB4	blood:	n/a	chr15:59157169-59157178
8	TCF12	chr15:59158321-59158845	A549	lung:	n/a	n/a
9	CBX3	chr15:59158322-59158859	K562	blood:	n/a	n/a
10	YY1	chr15:59158310-59158854	HepG2	liver:	n/a	n/a
11	POLR2A	chr15:59156643-59158751	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:59158040..59159719-chr15:59224699..59227685,2	MCF-7	breast:
2	chr15:59158172..59158742-chr20:25371320..25372132,2	HCT-116	colon:
3	chr15:59141477..59144121-chr15:59157896..59159549,2	MCF-7	breast:
4	chr15:59150365..59151946-chr15:59158006..59159550,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259353	TF binding region
ENSG00000242747	TF binding region
ENSG00000100997	Chromatin interaction
ENSG00000137776	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10518991	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10518992	0.97[EUR][1000 genomes]
rs1078001	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1092172	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11071401	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11630160	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11636723	0.97[EUR][1000 genomes]
rs11637077	0.97[EUR][1000 genomes]
rs11858989	0.97[EUR][1000 genomes]
rs12438918	0.81[EUR][1000 genomes]
rs12438961	0.84[EUR][1000 genomes]
rs12443436	0.89[EUR][1000 genomes]
rs12595482	0.94[EUR][1000 genomes]
rs12914723	0.94[EUR][1000 genomes]
rs17302038	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17302045	0.97[EUR][1000 genomes]
rs173214	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2013117	0.87[EUR][1000 genomes]
rs2279719	0.90[EUR][1000 genomes]
rs28473013	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28529423	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28538484	0.97[EUR][1000 genomes]
rs28641638	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28709922	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35477914	0.97[EUR][1000 genomes]
rs431414	0.94[EUR][1000 genomes]
rs592407	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs604057	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs637918	0.91[EUR][1000 genomes]
rs677933	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs694918	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173317	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8035628	0.93[EUR][1000 genomes]
rs813219	0.94[EUR][1000 genomes]
rs813220	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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	87 gene(s)	inside rSNPs	diseases
2	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1035640	chr15:59105360-59190930	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv904270	chr15:59140329-59238415	Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer 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	48 gene(s)	inside rSNPs	diseases
7	nsv977720	chr15:59157444-59165373	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59111800-59159600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:59120000-59169000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr15:59145000-59166600	Weak transcription	HSMMtube	muscle
4	chr15:59147200-59169000	Weak transcription	K562	blood
5	chr15:59147600-59174600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:59148000-59168600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:59148000-59169000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:59151200-59165400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:59154600-59170200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr15:59156800-59158400	Active TSS	Fetal Intestine Large	intestine
11	chr15:59156800-59158600	Active TSS	HepG2	liver
12	chr15:59157200-59158400	Active TSS	Fetal Intestine Small	intestine
13	chr15:59157200-59168600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:59157400-59168800	Weak transcription	Brain Angular Gyrus	brain
15	chr15:59157400-59170400	Weak transcription	Aorta	Aorta
16	chr15:59157600-59159600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:59157600-59169000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:59157600-59169400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr15:59157600-59169400	Weak transcription	Brain Germinal Matrix	brain
20	chr15:59157600-59170200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr15:59157600-59170200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:59157600-59170200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:59157600-59170200	Weak transcription	Fetal Brain Female	brain
24	chr15:59157800-59158600	Enhancers	Hela-S3	cervix
25	chr15:59157800-59158800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr15:59157800-59159400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:59157800-59159400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:59157800-59159600	Weak transcription	Spleen	Spleen
29	chr15:59157800-59169000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:59157800-59169400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:59157800-59169400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:59157800-59170000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:59157800-59170200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:59157800-59170200	Weak transcription	Primary T cells from cord blood	blood
35	chr15:59157800-59170400	Weak transcription	Primary B cells from cord blood	blood
36	chr15:59157800-59170400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr15:59157800-59172600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:59158000-59158400	Active TSS	Pancreas	Pancrea
39	chr15:59158000-59158800	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr15:59158000-59158800	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr15:59158000-59162600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:59158000-59162600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:59158000-59165400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:59158000-59165600	Weak transcription	Fetal Muscle Leg	muscle
45	chr15:59158000-59167600	Weak transcription	Thymus	Thymus
46	chr15:59158000-59168400	Weak transcription	Gastric	stomach
47	chr15:59158000-59168400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:59158000-59168800	Weak transcription	Adipose Nuclei	Adipose
49	chr15:59158000-59169000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:59158000-59169000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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