Variant report

Variant	rs17435932
Chromosome Location	chr15:49448012-49448013
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:514)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:514 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ETS1	chr15:49447785-49448196	K562	blood:	n/a	chr15:49447884-49447897 chr15:49447785-49447796
2	TAF7	chr15:49447570-49448173	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr15:49447563-49448084	PFSK-1	brain:	n/a	n/a
4	SIN3A	chr15:49447193-49448797	H1-hESC	embryonic stem cell:	n/a	chr15:49447881-49447889
5	HEY1	chr15:49447483-49448297	K562	blood:	n/a	n/a
6	POLR2A	chr15:49447239-49448344	Raji	blood:	n/a	n/a
7	POLR2A	chr15:49447468-49448248	K562	blood:	n/a	n/a
8	EP300	chr15:49447626-49448252	GM12878	blood:	n/a	n/a
9	SIX5	chr15:49447591-49448043	H1-hESC	embryonic stem cell:	n/a	n/a
10	HEY1	chr15:49447507-49448219	HepG2	liver:	n/a	n/a
11	REST	chr15:49447671-49448020	PANC-1	pancreas:	n/a	n/a
12	PAX5	chr15:49447567-49448087	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:49447121-49448221	K562	blood:	n/a	n/a
14	MAX	chr15:49447286-49448282	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr15:49447895-49448143	A549	lung:	n/a	n/a
16	POLR2A	chr15:49447914-49448186	GM12878	blood:	n/a	n/a
17	KAP1	chr15:49447742-49448041	K562	blood:	n/a	n/a
18	CUX1	chr15:49447719-49448233	K562	blood:	n/a	n/a
19	TAF1	chr15:49447517-49448187	GM12891	blood:	n/a	n/a
20	GABPA	chr15:49447666-49448118	Hela-S3	cervix:	n/a	n/a
21	USF1	chr15:49447786-49448035	A549	lung:	n/a	n/a
22	POLR2A	chr15:49447569-49448248	K562	blood:	n/a	n/a
23	SP1	chr15:49447644-49448087	GM12878	blood:	n/a	chr15:49447809-49447820 chr15:49447856-49447867 chr15:49447783-49447797
24	POLR2A	chr15:49447437-49448264	GM12892	blood:	n/a	n/a
25	ELF1	chr15:49447732-49448104	K562	blood:	n/a	n/a
26	YY1	chr15:49447029-49448296	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr15:49447247-49448332	ProgFib	skin:	n/a	n/a
28	MAX	chr15:49447235-49448202	K562	blood:	n/a	n/a
29	HDAC2	chr15:49447740-49448179	K562	blood:	n/a	n/a
30	MAZ	chr15:49447181-49448309	K562	blood:	n/a	n/a
31	MAX	chr15:49447371-49448328	ECC-1	luminal epithelium:	n/a	n/a
32	SIN3AK20	chr15:49447597-49448355	PFSK-1	brain:	n/a	n/a
33	GATA1	chr15:49447019-49448881	PBDE	blood:	n/a	n/a
34	POLR2A	chr15:49447596-49448161	SK-N-SH	brain:	n/a	n/a
35	CTCF	chr15:49447940-49448090	HUVEC	blood vessel:	n/a	n/a
36	BCLAF1	chr15:49447534-49448220	K562	blood:	n/a	chr15:49447824-49447833 chr15:49447881-49447889
37	CHD2	chr15:49447317-49448234	HepG2	liver:	n/a	n/a
38	POLR2A	chr15:49447252-49448288	K562	blood:	n/a	n/a
39	TBL1XR1	chr15:49447181-49448147	GM12878	blood:	n/a	n/a
40	POLR2A	chr15:49447502-49448224	GM12891	blood:	n/a	n/a
41	ARID3A	chr15:49447782-49448179	K562	blood:	n/a	n/a
42	BRCA1	chr15:49447785-49448174	GM12878	blood:	n/a	n/a
43	POLR2A	chr15:49447238-49448294	Gliobla	brain:	n/a	n/a
44	PBX3	chr15:49447496-49448245	SK-N-SH	brain:	n/a	n/a
45	GTF2F1	chr15:49447686-49448174	H1-hESC	embryonic stem cell:	n/a	n/a
46	TCF12	chr15:49447472-49448277	ECC-1	luminal epithelium:	n/a	n/a
47	CTCF	chr15:49448000-49448150	AG09319	gingival:	n/a	n/a
48	GABPA	chr15:49447541-49448239	GM12878	blood:	n/a	n/a
49	TAF1	chr15:49447537-49448206	H1-hESC	embryonic stem cell:	n/a	n/a
50	RCOR1	chr15:49447184-49448801	Hela-S3	cervix:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:49445500..49449019-chr15:49469042..49472548,3	K562	blood:
2	chr15:49443824..49452367-chr15:49460648..49465189,20	K562	blood:
3	chr15:49445500..49448180-chr15:49469776..49471285,2	K562	blood:
4	chr15:49446083..49452367-chr15:49460693..49464702,19	K562	blood:
5	chr15:49446471..49449731-chr15:49460521..49465602,13	MCF-7	breast:
6	chr15:49446244..49450190-chr15:50645448..50647621,4	K562	blood:

No data

Variant related genes	Relation type
NDUFAF4P1	TF binding region
COPS2	TF binding region
ENSG00000259545	Chromatin interaction
ENSG00000264210	Chromatin interaction
ENSG00000156958	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11853969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11854039	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854184	0.90[LWK][hapmap]
rs11854557	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11857515	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11857773	0.83[ASN][1000 genomes]
rs11858814	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12899422	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12900819	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12900838	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12901353	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901929	1.00[AFR][1000 genomes]
rs12902096	0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12902271	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12905094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12905477	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12914876	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs17393761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17472989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1961393	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2289389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2413926	0.84[CEU][hapmap]
rs34562714	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748066	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36100631	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4774538	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4775794	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4775806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775808	0.96[AFR][1000 genomes]
rs55979115	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62009762	0.85[ASN][1000 genomes]
rs62009834	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71467664	0.81[ASN][1000 genomes]
rs7164309	0.86[CEU][hapmap]
rs7180168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7497335	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8029687	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs8043493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9672848	0.81[AFR][1000 genomes]

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	nsv827332	chr15:49447726-49448176	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17435932	LCMT2	cis	parietal	SCAN
rs17435932	SPATA5L1	cis	parietal	SCAN
rs17435932	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49445400-49449000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr15:49445600-49449200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr15:49445800-49449000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr15:49445800-49449200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:49445800-49449200	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr15:49445800-49450400	Active TSS	NHLF	lung
7	chr15:49446000-49448800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:49446000-49449000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr15:49446000-49449400	Active TSS	K562	blood
10	chr15:49446000-49449600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:49446000-49450000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:49446200-49448800	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr15:49446200-49448800	Active TSS	Hela-S3	cervix
14	chr15:49446200-49449000	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr15:49446200-49449000	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr15:49446200-49449000	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr15:49446200-49449200	Active TSS	A549	lung
18	chr15:49446200-49449600	Active TSS	NHDF-Ad	bronchial
19	chr15:49446400-49449000	Active TSS	Muscle Satellite Cultured Cells	--
20	chr15:49446400-49449000	Active TSS	Right Atrium	heart
21	chr15:49446400-49449000	Active TSS	Osteobl	bone
22	chr15:49446400-49449200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:49446400-49449200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:49446400-49449600	Active TSS	HMEC	breast
25	chr15:49446400-49450400	Active TSS	GM12878-XiMat	blood
26	chr15:49446600-49448600	Active TSS	Fetal Lung	lung
27	chr15:49446600-49448600	Active TSS	Right Ventricle	heart
28	chr15:49446600-49448800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:49446600-49448800	Active TSS	Ovary	ovary
30	chr15:49446600-49449000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:49446600-49449000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:49446600-49449000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:49446600-49449000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:49446600-49449000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr15:49446600-49449000	Active TSS	Fetal Intestine Small	intestine
36	chr15:49446600-49449000	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr15:49446600-49449000	Active TSS	Fetal Muscle Leg	muscle
38	chr15:49446600-49449000	Active TSS	Psoas Muscle	Psoas
39	chr15:49446600-49449000	Active TSS	HSMM	muscle
40	chr15:49446600-49449000	Active TSS	HSMMtube	muscle
41	chr15:49446600-49449000	Active TSS	NHEK	skin
42	chr15:49446600-49449200	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr15:49446600-49449200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:49446600-49449200	Active TSS	Fetal Thymus	thymus
45	chr15:49446600-49449400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr15:49446600-49449600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:49446600-49450000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:49446800-49448200	Active TSS	Colon Smooth Muscle	Colon
49	chr15:49446800-49448400	Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr15:49446800-49448600	Active TSS	Brain Inferior Temporal Lobe	brain

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