Variant report

Variant	rs12462614
Chromosome Location	chr19:39687592-39687593
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:2)
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	MAX	chr19:39687478-39687960	ECC-1	luminal epithelium:	n/a	n/a
2	GABPA	chr19:39687546-39687949	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr19:39687467-39687788	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F6	chr19:39687471-39687821	K562	blood:	n/a	chr19:39687562-39687574
5	E2F6	chr19:39687467-39687891	K562	blood:	n/a	chr19:39687562-39687574
6	MAX	chr19:39687455-39687886	K562	blood:	n/a	n/a
7	E2F6	chr19:39687458-39687951	H1-hESC	embryonic stem cell:	n/a	chr19:39687562-39687574
8	TBP	chr19:39687554-39687715	H1-hESC	embryonic stem cell:	n/a	n/a
9	TEAD4	chr19:39687215-39687610	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr19:39687517-39687801	SK-N-SH	brain:	n/a	n/a
11	ZNF263	chr19:39687469-39687604	HEK293-T-REx	kidney:	n/a	chr19:39687486-39687507
12	MAX	chr19:39687478-39687742	K562	blood:	n/a	n/a
13	SIN3A	chr19:39687132-39687779	H1-hESC	embryonic stem cell:	n/a	n/a
14	E2F6	chr19:39687527-39687792	K562	blood:	n/a	chr19:39687562-39687574
15	MAX	chr19:39687416-39688128	H1-hESC	embryonic stem cell:	n/a	n/a
16	MXI1	chr19:39687586-39687783	H1-hESC	embryonic stem cell:	n/a	n/a
17	TEAD4	chr19:39687223-39687685	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr19:39687460-39687841	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr19:39687429-39687959	H1-hESC	embryonic stem cell:	n/a	n/a
20	CBX3	chr19:39687495-39687770	K562	blood:	n/a	n/a
21	TCF12	chr19:39687526-39687710	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr19:39687511-39687764	K562	blood:	n/a	n/a
23	MAX	chr19:39687460-39687885	SK-N-SH	brain:	n/a	n/a
24	E2F6	chr19:39687280-39688069	H1-hESC	embryonic stem cell:	n/a	chr19:39687562-39687574
25	CHD2	chr19:39687586-39687706	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:39687568-39687618	PFSK-1	brain:	n/a
2	chr19:39687568-39687618	PANC-1	pancreas:	n/a
3	chr19:39687568-39687618	RPTEC	kidney:	n/a
4	chr19:39687568-39687618	GM06990	blood:	n/a
5	chr19:39687568-39687618	SK-N-SH	brain:	n/a
6	chr19:39687568-39687618	HCF	heart:	n/a
7	chr19:39687568-39687618	U87	brain:	n/a
8	chr19:39687568-39687618	HRCEpiC	kidney:	n/a
9	chr19:39687568-39687618	HAEpiC	amniotic membrane:	n/a
10	chr19:39687568-39687618	NB4	blood:	n/a
11	chr19:39687568-39687618	HRPEpiC	eye:	n/a
12	chr19:39687568-39687618	H1-hESC	embryonic stem cell:	embryo
13	chr19:39687568-39687618	GM12878	blood:	n/a
14	chr19:39687568-39687618	HNPCEpiC	eye:	n/a
15	chr19:39687568-39687618	BE2_C	brain:	n/a
16	chr19:39687568-39687618	LNCaP	prostate:	n/a
17	chr19:39687568-39687618	GM19239	blood:	n/a
18	chr19:39687568-39687618	HEK293	kidney:	embryo
19	chr19:39687568-39687618	HCPEpiC	choroid plexus:	n/a
20	chr19:39687568-39687618	HPAEpiC	pulmonary alveolar:	n/a
21	chr19:39687568-39687618	HepG2	liver:	n/a
22	chr19:39687568-39687618	HRE	kidney:	n/a
23	chr19:39687568-39687618	Jurkat	blood:	n/a
24	chr19:39687568-39687618	HL-60	blood:	n/a
25	chr19:39687568-39687618	NHBE	bronchial:	n/a
26	chr19:39687568-39687618	NT2-D1	testis:	n/a
27	chr19:39687568-39687618	NH-A	brain:	n/a
28	chr19:39687568-39687618	Caco-2	colon:	n/a
29	chr19:39687568-39687618	BJ	skin:	n/a
30	chr19:39687568-39687618	SK-N-MC	brain:	n/a
31	chr19:39687568-39687618	AG10803	skin:	n/a
32	chr19:39687568-39687618	HCM	heart:	n/a
33	chr19:39687568-39687618	PrEC	prostate:	n/a
34	chr19:39687568-39687618	GM12892	blood:	n/a
35	chr19:39687568-39687618	HEEpiC	esophagus:	n/a
36	chr19:39687568-39687618	HMEC	breast:	n/a
37	chr19:39687568-39687618	ECC-1	luminal epithelium:	n/a
38	chr19:39687568-39687618	K562	blood:	n/a
39	chr19:39687568-39687618	T-47D	breast:	n/a
40	chr19:39687568-39687618	IMR90	lung:	fetal
41	chr19:39687568-39687618	MCF-7	breast:	n/a
42	chr19:39687568-39687618	AG09309	skin:	n/a
43	chr19:39687568-39687618	SAEC	small airway:	n/a
44	chr19:39687568-39687618	AG09319	gingival:	n/a
45	chr19:39687568-39687618	SKMC	muscle:	n/a
46	chr19:39687568-39687618	ProgFib	skin:	n/a
47	chr19:39687568-39687618	HUVEC	blood vessel:	n/a
48	chr19:39687568-39687618	Hepatocyte	liver:	n/a
49	chr19:39687568-39687618	HCT-116	colon:	n/a
50	chr19:39687568-39687618	HIPEpiC	eye:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39687448..39690003-chr19:39693268..39695758,2	K562	blood:
2	chr19:39615011..39617919-chr19:39686746..39689965,3	MCF-7	breast:

No data

Variant related genes	Relation type
NCCRP1	TF binding region
NCCRP1	CpG island
ENSG00000130669	Chromatin interaction
ENSG00000179751	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11083511	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083512	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083513	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083514	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11668945	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672471	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672475	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672479	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11672787	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12609028	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12609203	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12610064	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12610093	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12610618	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12974074	0.87[CHB][hapmap]
rs12974792	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12976040	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1808652	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2013626	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2319154	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2319155	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2319156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2873914	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58016205	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58278424	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7508321	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8100659	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8103222	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8103224	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106521	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs892015	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs892016	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv1796470	chr19:39679379-39714631	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12462614	ZNF229	cis	parietal	SCAN
rs12462614	B9D2	cis	cerebellum	SCAN
rs12462614	B9D2	cis	parietal	SCAN
rs12462614	CCDC8	cis	parietal	SCAN
rs12462614	ZNF229	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39657800-39687600	Weak transcription	Right Atrium	heart
2	chr19:39685000-39690000	Enhancers	A549	lung
3	chr19:39685400-39687600	Enhancers	Pancreas	Pancrea
4	chr19:39685400-39688800	Bivalent Enhancer	Placenta	Placenta
5	chr19:39685600-39688000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:39685600-39688200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
7	chr19:39685600-39688200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
8	chr19:39685600-39688200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
9	chr19:39685800-39688200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr19:39686000-39687600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:39686000-39687600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:39686000-39688200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:39686000-39688400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:39686200-39688000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:39686200-39688000	Weak transcription	Hela-S3	cervix
16	chr19:39686400-39688400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr19:39686600-39688000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr19:39686600-39688000	Bivalent Enhancer	NHEK	skin
19	chr19:39686600-39688200	Bivalent Enhancer	Fetal Intestine Small	intestine
20	chr19:39686800-39687600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
21	chr19:39686800-39687600	Bivalent Enhancer	Fetal Stomach	stomach
22	chr19:39686800-39688000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:39686800-39688000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr19:39686800-39688200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
25	chr19:39686800-39688400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:39686800-39693200	Weak transcription	Gastric	stomach
27	chr19:39687000-39687600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:39687000-39687600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
29	chr19:39687000-39687600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:39687000-39687600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:39687000-39687600	Bivalent Enhancer	Colonic Mucosa	Colon
32	chr19:39687000-39688000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
33	chr19:39687000-39688000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:39687000-39688000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
35	chr19:39687000-39688000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
36	chr19:39687000-39688000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
37	chr19:39687000-39688000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr19:39687000-39688000	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr19:39687000-39688200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:39687200-39687600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:39687200-39687600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
42	chr19:39687200-39687600	Active TSS	Esophagus	oesophagus
43	chr19:39687200-39687800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:39687200-39688000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
45	chr19:39687200-39688200	Active TSS	H9 Cell Line	embryonic stem cell
46	chr19:39687200-39688200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
47	chr19:39687200-39688600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
48	chr19:39687400-39687600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:39687400-39687600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:39687400-39687600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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