Variant report

Variant	rs12440159
Chromosome Location	chr15:75188584-75188585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75187779-75190960	K562	blood:	n/a	n/a
2	POLR2A	chr15:75188040-75188916	U87	brain:	n/a	n/a
3	POLR2A	chr15:75187739-75194836	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr15:75188380-75188599	MCF-7	breast:	n/a	n/a
5	POLR2A	chr15:75188500-75189063	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr15:75187943-75190750	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr15:75188444-75188930	HepG2	liver:	n/a	n/a
8	POLR2A	chr15:75188318-75189077	HepG2	liver:	n/a	n/a
9	POLR2A	chr15:75188574-75188982	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:75188189-75190877	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:75188363-75190846	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr15:75188291-75189022	HL-60	blood:	n/a	n/a
13	POLR2A	chr15:75188344-75189075	HepG2	liver:	n/a	n/a
14	POLR2A	chr15:75187964-75190840	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr15:75188042-75189226	HCT-116	colon:	n/a	n/a
16	POLR2A	chr15:75188309-75190832	GM12891	blood:	n/a	n/a
17	POLR2A	chr15:75187990-75189019	A549	lung:	n/a	n/a
18	POLR2A	chr15:75188017-75190928	K562	blood:	n/a	n/a
19	POLR2A	chr15:75188513-75188953	A549	lung:	n/a	n/a
20	POLR2A	chr15:75188534-75188969	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr15:75188103-75188973	GM12891	blood:	n/a	n/a
22	POLR2A	chr15:75188187-75190911	K562	blood:	n/a	n/a
23	POLR2A	chr15:75187473-75194577	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr15:75187941-75190956	HepG2	liver:	n/a	n/a
25	POLR2A	chr15:75188440-75189117	K562	blood:	n/a	n/a
26	POLR2A	chr15:75187279-75194196	HepG2	liver:	n/a	n/a
27	POLR2A	chr15:75188313-75190881	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr15:75188157-75190930	GM12878	blood:	n/a	n/a
29	POLR2A	chr15:75188079-75191035	GM12892	blood:	n/a	n/a
30	STAT5A	chr15:75188562-75188908	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:75188563-75190883	K562	blood:	n/a	n/a
32	POLR2A	chr15:75188404-75188907	A549	lung:	n/a	n/a
33	POLR2A	chr15:75187680-75194520	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr15:75188556-75193697	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr15:75188170-75190915	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr15:75188445-75189039	GM12878	blood:	n/a	n/a
37	POLR2A	chr15:75188403-75188983	GM12892	blood:	n/a	n/a
38	POLR2A	chr15:75187997-75188916	U87	brain:	n/a	n/a
39	POLR2A	chr15:75188118-75190973	PANC-1	pancreas:	n/a	n/a
40	POLR2A	chr15:75187885-75191046	H1-hESC	embryonic stem cell:	n/a	n/a
41	BCL3	chr15:75188558-75190980	A549	lung:	n/a	n/a
42	POLR2A	chr15:75188444-75190873	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr15:75187813-75190893	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr15:75188297-75190792	GM12878	blood:	n/a	n/a
45	POLR2A	chr15:75188242-75189010	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr15:75188292-75188854	GM12878	blood:	n/a	n/a
47	POLR2A	chr15:75188034-75193326	PFSK-1	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
2	chr15:74911034..74913432-chr15:75186630..75189281,2	MCF-7	breast:
3	chr15:75145656..75148535-chr15:75188097..75189916,2	K562	blood:
4	chr15:75133989..75136127-chr15:75187296..75189781,2	K562	blood:
5	chr15:75188520..75190057-chr15:75227191..75229624,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260824	TF binding region
ENSG00000140497	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000140474	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12437831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12439641	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12441499	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs12441758	0.93[AMR][1000 genomes]
rs12442804	0.91[ASN][1000 genomes]
rs28726277	1.00[ASN][1000 genomes]
rs3935818	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs4886635	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57498691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60494786	0.81[ASN][1000 genomes]
rs60698434	1.00[ASN][1000 genomes]
rs7179093	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs729263	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 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	chr15:75183200-75189400	Weak transcription	Psoas Muscle	Psoas
2	chr15:75183200-75191600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:75183200-75192000	Weak transcription	Fetal Kidney	kidney
4	chr15:75183200-75192400	Weak transcription	HUVEC	blood vessel
5	chr15:75183200-75197600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:75183400-75192200	Weak transcription	NH-A	brain
7	chr15:75183600-75193800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:75183600-75193800	Strong transcription	Fetal Stomach	stomach
9	chr15:75183800-75189200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:75184000-75195400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:75184200-75192400	Weak transcription	Fetal Brain Male	brain
12	chr15:75184200-75196600	Weak transcription	Small Intestine	intestine
13	chr15:75185000-75193800	Strong transcription	Fetal Intestine Small	intestine
14	chr15:75185000-75194800	Weak transcription	Right Atrium	heart
15	chr15:75185200-75188600	Strong transcription	Fetal Muscle Leg	muscle
16	chr15:75185200-75193800	Strong transcription	Fetal Intestine Large	intestine
17	chr15:75185200-75197000	Weak transcription	Fetal Heart	heart
18	chr15:75185800-75190000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:75185800-75191200	Weak transcription	Aorta	Aorta
20	chr15:75185800-75192600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:75186000-75188600	Weak transcription	Brain Angular Gyrus	brain
22	chr15:75186000-75188600	Weak transcription	Gastric	stomach
23	chr15:75186000-75189600	Weak transcription	Ovary	ovary
24	chr15:75186200-75188600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:75186200-75188600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:75186200-75188600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:75186200-75188600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:75186200-75188600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:75186200-75188600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:75186200-75188600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr15:75186200-75188600	Weak transcription	Pancreas	Pancrea
32	chr15:75186200-75188600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:75186200-75188800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr15:75186200-75188800	Weak transcription	Fetal Lung	lung
35	chr15:75186200-75188800	Weak transcription	Osteobl	bone
36	chr15:75186200-75189200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr15:75186200-75189400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:75186200-75189400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr15:75186200-75189600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:75186200-75189600	Weak transcription	Esophagus	oesophagus
41	chr15:75186200-75189600	Weak transcription	Left Ventricle	heart
42	chr15:75186200-75191200	Weak transcription	Placenta	Placenta
43	chr15:75186200-75191200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr15:75186200-75191600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:75186200-75192000	Weak transcription	NHDF-Ad	bronchial
46	chr15:75186200-75192400	Weak transcription	Colon Smooth Muscle	Colon
47	chr15:75186200-75193600	Weak transcription	Stomach Mucosa	stomach
48	chr15:75186400-75188600	Weak transcription	NHEK	skin
49	chr15:75186400-75189200	Weak transcription	HMEC	breast
50	chr15:75186400-75191600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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