Variant report

Variant	rs11666474
Chromosome Location	chr19:52673401-52673402
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:52673362-52673412	AG09309	skin:	n/a
2	chr19:52673362-52673412	ProgFib	skin:	n/a
3	chr19:52673362-52673412	K562	blood:	n/a
4	chr19:52673362-52673412	PrEC	prostate:	n/a
5	chr19:52673362-52673412	HRCEpiC	kidney:	n/a
6	chr19:52673362-52673412	PANC-1	pancreas:	n/a
7	chr19:52673362-52673412	LNCaP	prostate:	n/a
8	chr19:52673362-52673412	AG04450	lung:	fetal
9	chr19:52673362-52673412	HAEpiC	amniotic membrane:	n/a
10	chr19:52673362-52673412	NT2-D1	testis:	n/a
11	chr19:52673362-52673412	HRE	kidney:	n/a
12	chr19:52673362-52673412	H1-hESC	embryonic stem cell:	embryo
13	chr19:52673362-52673412	HNPCEpiC	eye:	n/a
14	chr19:52673362-52673412	HPAEpiC	pulmonary alveolar:	n/a
15	chr19:52673362-52673412	GM06990	blood:	n/a
16	chr19:52673362-52673412	BJ	skin:	n/a
17	chr19:52673362-52673412	HCT-116	colon:	n/a
18	chr19:52673362-52673412	ECC-1	luminal epithelium:	n/a
19	chr19:52673362-52673412	CMK	blood:	n/a
20	chr19:52673362-52673412	HL-60	blood:	n/a
21	chr19:52673362-52673412	Jurkat	blood:	n/a
22	chr19:52673362-52673412	U87	brain:	n/a
23	chr19:52673362-52673412	AG04449	skin:	fetal
24	chr19:52673362-52673412	NHBE	bronchial:	n/a
25	chr19:52673362-52673412	HIPEpiC	eye:	n/a
26	chr19:52673362-52673412	BE2_C	brain:	n/a
27	chr19:52673362-52673412	MCF-7	breast:	n/a
28	chr19:52673362-52673412	Caco-2	colon:	n/a
29	chr19:52673362-52673412	GM12878	blood:	n/a
30	chr19:52673362-52673412	NB4	blood:	n/a
31	chr19:52673362-52673412	HCPEpiC	choroid plexus:	n/a
32	chr19:52673362-52673412	MCF10A-Er-Src	breast:	n/a
33	chr19:52673362-52673412	PFSK-1	brain:	n/a
34	chr19:52673362-52673412	HUVEC	blood vessel:	n/a
35	chr19:52673362-52673412	HepG2	liver:	n/a
36	chr19:52673362-52673412	GM12891	blood:	n/a
37	chr19:52673362-52673412	SAEC	small airway:	n/a
38	chr19:52673362-52673412	AG09319	gingival:	n/a
39	chr19:52673362-52673412	IMR90	lung:	fetal
40	chr19:52673362-52673412	HMEC	breast:	n/a
41	chr19:52673362-52673412	GM12892	blood:	n/a
42	chr19:52673362-52673412	SK-N-SH_RA	brain:	n/a
43	chr19:52673362-52673412	HCM	heart:	n/a
44	chr19:52673362-52673412	NHDF-neo	bronchial:	n/a
45	chr19:52673362-52673412	AoSMC	blood vessel:	n/a
46	chr19:52673362-52673412	HEEpiC	esophagus:	n/a
47	chr19:52673362-52673412	A549	lung:	n/a
48	chr19:52673362-52673412	AG10803	skin:	n/a
49	chr19:52673362-52673412	HRPEpiC	eye:	n/a
50	chr19:52673362-52673412	ovcar-3	ovarian:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr19:52671404..52675593-chr19:52690586..52694996,6	MCF-7	breast:
2	chr19:52672624..52674722-chr2:220324070..220326972,2	MCF-7	breast:
3	chr19:52641011..52643212-chr19:52671736..52674683,3	MCF-7	breast:
4	chr19:52641278..52644856-chr19:52672246..52674908,4	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF836	CpG island
ENSG00000267927	CpG island
ENSG00000204611	Chromatin interaction
ENSG00000105568	Chromatin interaction
ENSG00000072195	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs35715660	0.90[EUR][1000 genomes]
rs8111199	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs919268	1.00[CEU][hapmap];0.91[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	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv580007	chr19:52660279-52693277	Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1059417	chr19:52662380-52703801	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv2760529	chr19:52662380-52703813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11666474	NLRP12	cis	cerebellum	SCAN
rs11666474	ZBTB45	cis	parietal	SCAN
rs11666474	KIR3DX1	cis	cerebellum	SCAN
rs11666474	ZNF628	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52663600-52673600	Weak transcription	Psoas Muscle	Psoas
2	chr19:52669000-52673600	Weak transcription	Aorta	Aorta
3	chr19:52669000-52673600	Weak transcription	Colonic Mucosa	Colon
4	chr19:52669000-52674000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:52671800-52673600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:52672200-52673600	Weak transcription	Gastric	stomach
7	chr19:52672200-52673600	Weak transcription	Lung	lung
8	chr19:52672200-52673600	Weak transcription	HSMM	muscle
9	chr19:52672800-52673600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr19:52672800-52673600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr19:52672800-52673800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:52673000-52673600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr19:52673000-52673600	Enhancers	Primary T cells from cord blood	blood
14	chr19:52673000-52673600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr19:52673000-52673600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:52673000-52673800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:52673000-52673800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr19:52673000-52674000	Flanking Active TSS	Brain Germinal Matrix	brain
19	chr19:52673000-52675200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:52673000-52675200	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr19:52673000-52675200	Active TSS	HSMMtube	muscle
22	chr19:52673200-52673600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
23	chr19:52673200-52673600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr19:52673200-52673600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:52673200-52673600	Enhancers	Primary B cells from cord blood	blood
26	chr19:52673200-52673600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr19:52673200-52673600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:52673200-52673600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:52673200-52673600	Enhancers	Liver	Liver
30	chr19:52673200-52673600	Flanking Active TSS	Fetal Brain Female	brain
31	chr19:52673200-52673600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr19:52673200-52673800	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr19:52673200-52673800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
34	chr19:52673200-52674000	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr19:52673200-52674000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr19:52673200-52674200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr19:52673200-52674600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr19:52673200-52675000	Active TSS	Fetal Kidney	kidney
39	chr19:52673200-52675000	Active TSS	GM12878-XiMat	blood
40	chr19:52673200-52675600	Active TSS	Muscle Satellite Cultured Cells	--
41	chr19:52673200-52675600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr19:52673200-52675600	Active TSS	HMEC	breast
43	chr19:52673200-52675600	Active TSS	NHDF-Ad	bronchial
44	chr19:52673400-52673600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
45	chr19:52673400-52673600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:52673400-52673600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:52673400-52673600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr19:52673400-52673600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:52673400-52673600	Enhancers	Primary hematopoietic stem cells	blood
50	chr19:52673400-52673600	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links