Variant report

Variant	rs12441342
Chromosome Location	chr15:40331914-40331915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr15:40330815-40331994	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:40331057-40331933	GM18505	blood:	n/a	n/a
3	GABPA	chr15:40330707-40331988	SK-N-SH	brain:	n/a	chr15:40331471-40331480
4	POLR2A	chr15:40330654-40331916	K562	blood:	n/a	n/a
5	GABPA	chr15:40330649-40331947	A549	lung:	n/a	chr15:40331471-40331480
6	MXI1	chr15:40330015-40331992	SK-N-SH	brain:	n/a	n/a
7	MAX	chr15:40330871-40331989	ECC-1	luminal epithelium:	n/a	chr15:40331461-40331471
8	TAF1	chr15:40330967-40331922	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr15:40331006-40331924	U87	brain:	n/a	n/a
10	GABPA	chr15:40330834-40331926	HL-60	blood:	n/a	chr15:40331471-40331480
11	POLR2A	chr15:40329864-40331947	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr15:40330394-40331991	GM12878	blood:	n/a	n/a
13	HCFC1	chr15:40329972-40331977	Hela-S3	cervix:	n/a	n/a
14	REST	chr15:40330225-40332007	H1-neurons	neurons:	n/a	n/a
15	POLR2A	chr15:40330863-40331928	HepG2	liver:	n/a	n/a
16	POLR2A	chr15:40330595-40331947	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr15:40331054-40331921	K562	blood:	n/a	n/a
18	GABPA	chr15:40330693-40331969	SK-N-SH	brain:	n/a	chr15:40331471-40331480
19	STAT5A	chr15:40331011-40331934	GM12878	blood:	n/a	chr15:40331466-40331478 chr15:40331462-40331474
20	POLR2A	chr15:40330916-40331915	HUVEC	blood vessel:	n/a	n/a
21	GABPA	chr15:40330566-40332023	MCF-7	breast:	n/a	chr15:40331471-40331480
22	POLR2A	chr15:40331000-40331954	U87	brain:	n/a	n/a
23	PML	chr15:40330864-40331927	GM12878	blood:	n/a	n/a
24	MYC	chr15:40331099-40331928	K562	blood:	n/a	chr15:40331461-40331471
25	POLR2A	chr15:40330486-40331990	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:40331866-40331916	SK-N-MC	brain:	n/a
2	chr15:40331866-40331916	NHDF-neo	bronchial:	n/a
3	chr15:40331866-40331916	RPTEC	kidney:	n/a
4	chr15:40331866-40331916	HCPEpiC	choroid plexus:	n/a
5	chr15:40331866-40331916	Caco-2	colon:	n/a
6	chr15:40331866-40331916	AG10803	skin:	n/a
7	chr15:40331866-40331916	SK-N-SH_RA	brain:	n/a
8	chr15:40331866-40331916	HPAEpiC	pulmonary alveolar:	n/a
9	chr15:40331866-40331916	MCF-7	breast:	n/a
10	chr15:40331866-40331916	PANC-1	pancreas:	n/a
11	chr15:40331866-40331916	HEK293	kidney:	embryo
12	chr15:40331866-40331916	K562	blood:	n/a
13	chr15:40331866-40331916	NT2-D1	testis:	n/a
14	chr15:40331866-40331916	HIPEpiC	eye:	n/a
15	chr15:40331866-40331916	GM12892	blood:	n/a
16	chr15:40331866-40331916	HMEC	breast:	n/a
17	chr15:40331866-40331916	AG04450	lung:	fetal
18	chr15:40331866-40331916	ovcar-3	ovarian:	n/a
19	chr15:40331866-40331916	Hela-S3	cervix:	n/a
20	chr15:40331866-40331916	HL-60	blood:	n/a
21	chr15:40331866-40331916	H1-hESC	embryonic stem cell:	embryo
22	chr15:40331866-40331916	AoSMC	blood vessel:	n/a
23	chr15:40331866-40331916	NHBE	bronchial:	n/a
24	chr15:40331866-40331916	HNPCEpiC	eye:	n/a
25	chr15:40331866-40331916	HRCEpiC	kidney:	n/a
26	chr15:40331866-40331916	U87	brain:	n/a
27	chr15:40331866-40331916	HRE	kidney:	n/a
28	chr15:40331866-40331916	SAEC	small airway:	n/a
29	chr15:40331866-40331916	NB4	blood:	n/a
30	chr15:40331866-40331916	PrEC	prostate:	n/a
31	chr15:40331866-40331916	PFSK-1	brain:	n/a
32	chr15:40331866-40331916	HUVEC	blood vessel:	n/a
33	chr15:40331866-40331916	AG09319	gingival:	n/a
34	chr15:40331866-40331916	BE2_C	brain:	n/a
35	chr15:40331866-40331916	GM12891	blood:	n/a
36	chr15:40331866-40331916	A549	lung:	n/a
37	chr15:40331866-40331916	GM06990	blood:	n/a
38	chr15:40331866-40331916	AG04449	skin:	fetal
39	chr15:40331866-40331916	HEEpiC	esophagus:	n/a
40	chr15:40331866-40331916	NH-A	brain:	n/a
41	chr15:40331866-40331916	HCF	heart:	n/a
42	chr15:40331866-40331916	BJ	skin:	n/a
43	chr15:40331866-40331916	CMK	blood:	n/a
44	chr15:40331866-40331916	LNCaP	prostate:	n/a
45	chr15:40331866-40331916	Hepatocyte	liver:	n/a
46	chr15:40331866-40331916	MCF10A-Er-Src	breast:	n/a
47	chr15:40331866-40331916	AG09309	skin:	n/a
48	chr15:40331866-40331916	ProgFib	skin:	n/a
49	chr15:40331866-40331916	IMR90	lung:	fetal
50	chr15:40331866-40331916	HepG2	liver:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr15:40331646..40335428-chr15:40336590..40339827,4	K562	blood:
2	chr15:40329348..40332922-chr15:40394377..40398986,5	MCF-7	breast:
3	chr15:40330945..40332578-chr15:40397344..40399517,2	K562	blood:
4	chr15:40320931..40323149-chr15:40329689..40332182,2	MCF-7	breast:

No data

Variant related genes	Relation type
SRP14	TF binding region
SRP14	CpG island
ENSG00000104081	Chromatin interaction
ENSG00000128829	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2291622	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2898985	0.94[ASN][1000 genomes]
rs3986354	0.80[ASN][1000 genomes]
rs4432245	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs711906	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8042947	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40330000-40332000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr15:40330000-40332000	Active TSS	Ovary	ovary
3	chr15:40330000-40332200	Active TSS	Left Ventricle	heart
4	chr15:40330000-40332400	Active TSS	Right Atrium	heart
5	chr15:40330200-40332000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr15:40330200-40332000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr15:40330200-40332000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:40330200-40332000	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr15:40330200-40332000	Active TSS	Gastric	stomach
10	chr15:40330200-40332200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:40330200-40332200	Active TSS	NHDF-Ad	bronchial
12	chr15:40330200-40332200	Active TSS	NHLF	lung
13	chr15:40330200-40332400	Active TSS	Colonic Mucosa	Colon
14	chr15:40330400-40332000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:40330400-40332000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:40330400-40332000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr15:40330400-40332000	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr15:40330400-40332000	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr15:40330400-40332000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:40330400-40332000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:40330400-40332000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:40330400-40332000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:40330400-40332000	Active TSS	Esophagus	oesophagus
24	chr15:40330400-40332000	Active TSS	Fetal Intestine Small	intestine
25	chr15:40330400-40332000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr15:40330400-40332000	Active TSS	Fetal Stomach	stomach
27	chr15:40330400-40332000	Active TSS	Lung	lung
28	chr15:40330400-40332000	Active TSS	Right Ventricle	heart
29	chr15:40330400-40332000	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr15:40330400-40332200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:40330400-40332200	Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr15:40330400-40332200	Active TSS	Muscle Satellite Cultured Cells	--
33	chr15:40330400-40332200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:40330400-40332200	Active TSS	Fetal Intestine Large	intestine
35	chr15:40330400-40332400	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr15:40330400-40332400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:40330400-40332400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:40330400-40332400	Active TSS	Psoas Muscle	Psoas
39	chr15:40330400-40332400	Active TSS	GM12878-XiMat	blood
40	chr15:40330400-40332600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:40330400-40332600	Active TSS	A549	lung
42	chr15:40330600-40332000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:40330600-40332000	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr15:40330600-40332000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr15:40330600-40332000	Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr15:40330600-40332000	Active TSS	Brain Anterior Caudate	brain
47	chr15:40330600-40332000	Active TSS	Brain Cingulate Gyrus	brain
48	chr15:40330600-40332000	Active TSS	Colon Smooth Muscle	Colon
49	chr15:40330600-40332000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr15:40330600-40332000	Active TSS	Fetal Kidney	kidney

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