Variant report

Variant	rs11112414
Chromosome Location	chr12:105613957-105613958
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:105613900-105614050	AoAF	blood vessel:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:105613925-105613975	HMEC	breast:	n/a
2	chr12:105613925-105613975	HL-60	blood:	n/a
3	chr12:105613925-105613975	AG10803	skin:	n/a
4	chr12:105613925-105613975	GM06990	blood:	n/a
5	chr12:105613925-105613975	ECC-1	luminal epithelium:	n/a
6	chr12:105613925-105613975	GM12892	blood:	n/a
7	chr12:105613925-105613975	HCF	heart:	n/a
8	chr12:105613925-105613975	NHBE	bronchial:	n/a
9	chr12:105613925-105613975	A549	lung:	n/a
10	chr12:105613925-105613975	RPTEC	kidney:	n/a
11	chr12:105613925-105613975	HAEpiC	amniotic membrane:	n/a
12	chr12:105613925-105613975	SK-N-SH_RA	brain:	n/a
13	chr12:105613925-105613975	GM19239	blood:	n/a
14	chr12:105613925-105613975	SAEC	small airway:	n/a
15	chr12:105613925-105613975	HCPEpiC	choroid plexus:	n/a
16	chr12:105613925-105613975	AG04449	skin:	fetal
17	chr12:105613925-105613975	MCF10A-Er-Src	breast:	n/a
18	chr12:105613925-105613975	LNCaP	prostate:	n/a
19	chr12:105613925-105613975	Hela-S3	cervix:	n/a
20	chr12:105613925-105613975	PrEC	prostate:	n/a
21	chr12:105613925-105613975	IMR90	lung:	fetal
22	chr12:105613925-105613975	K562	blood:	n/a
23	chr12:105613925-105613975	HCT-116	colon:	n/a
24	chr12:105613925-105613975	MCF-7	breast:	n/a
25	chr12:105613925-105613975	PFSK-1	brain:	n/a
26	chr12:105613925-105613975	HIPEpiC	eye:	n/a
27	chr12:105613925-105613975	PANC-1	pancreas:	n/a
28	chr12:105613925-105613975	SKMC	muscle:	n/a
29	chr12:105613925-105613975	U87	brain:	n/a
30	chr12:105613925-105613975	HRPEpiC	eye:	n/a
31	chr12:105613925-105613975	SK-N-SH	brain:	n/a
32	chr12:105613925-105613975	HRCEpiC	kidney:	n/a
33	chr12:105613925-105613975	GM12891	blood:	n/a
34	chr12:105613925-105613975	NB4	blood:	n/a
35	chr12:105613925-105613975	Jurkat	blood:	n/a
36	chr12:105613925-105613975	NHDF-neo	bronchial:	n/a
37	chr12:105613925-105613975	BJ	skin:	n/a
38	chr12:105613925-105613975	ovcar-3	ovarian:	n/a
39	chr12:105613925-105613975	HCM	heart:	n/a
40	chr12:105613925-105613975	HEK293	kidney:	embryo
41	chr12:105613925-105613975	CMK	blood:	n/a
42	chr12:105613925-105613975	AoSMC	blood vessel:	n/a
43	chr12:105613925-105613975	T-47D	breast:	n/a
44	chr12:105613925-105613975	HUVEC	blood vessel:	n/a
45	chr12:105613925-105613975	Caco-2	colon:	n/a
46	chr12:105613925-105613975	HepG2	liver:	n/a
47	chr12:105613925-105613975	HNPCEpiC	eye:	n/a
48	chr12:105613925-105613975	Hepatocyte	liver:	n/a
49	chr12:105613925-105613975	ProgFib	skin:	n/a
50	chr12:105613925-105613975	SK-N-MC	brain:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr12:105604459..105610765-chr12:105612400..105619000,9	MCF-7	breast:
2	chr12:105608691..105610894-chr12:105612066..105614500,4	MCF-7	breast:
3	chr12:105610784..105617210-chr12:105628529..105631630,8	MCF-7	breast:
4	chr12:105606795..105619301-chr12:105624368..105633184,26	MCF-7	breast:

No data

Variant related genes	Relation type
APPL2	TF binding region
APPL2	CpG island
ENSG00000136044	Chromatin interaction
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10861327	0.81[CHD][hapmap]
rs11112347	0.81[CHD][hapmap]
rs1196750	0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1196766	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1196767	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1196768	0.89[JPT][hapmap]
rs1196781	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs1196788	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs1196796	0.90[JPT][hapmap]
rs1196803	0.80[ASN][1000 genomes]
rs1196804	0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1196812	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1196814	0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs1196816	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1196836	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs1196838	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1196840	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs1196854	0.84[ASN][1000 genomes]
rs1196855	0.82[ASN][1000 genomes]
rs1196856	0.84[ASN][1000 genomes]
rs1196858	0.84[ASN][1000 genomes]
rs1196860	0.84[ASN][1000 genomes]
rs1196865	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1196866	0.83[ASN][1000 genomes]
rs1196867	0.83[ASN][1000 genomes]
rs1196868	0.82[ASN][1000 genomes]
rs1196870	0.80[ASN][1000 genomes]
rs1196876	0.80[ASN][1000 genomes]
rs1196877	0.80[ASN][1000 genomes]
rs1196878	0.81[ASN][1000 genomes]
rs1196883	0.82[CHD][hapmap]
rs1201657	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1201658	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs1317941	0.93[EUR][1000 genomes]
rs1732378	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1732379	0.83[ASN][1000 genomes]
rs1732384	0.81[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs2264066	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2374448	0.91[CHD][hapmap];0.91[JPT][hapmap]
rs2440708	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2440713	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2440717	0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2440719	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs727888	0.91[JPT][hapmap]
rs7310488	0.94[JPT][hapmap]
rs9143	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[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	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats 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	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11112414	APPL2	cis	cerebellum	SCAN
rs11112414	KIAA1033	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:105571400-105617800	Weak transcription	K562	blood
4	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:105578200-105620000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:105590200-105620000	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:105590400-105618800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr12:105591000-105619400	Strong transcription	Primary T cells from cord blood	blood
11	chr12:105594400-105614400	Weak transcription	Small Intestine	intestine
12	chr12:105595000-105618800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:105595800-105616600	Strong transcription	Primary hematopoietic stem cells	blood
14	chr12:105596000-105617000	Strong transcription	Fetal Lung	lung
15	chr12:105596400-105621800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:105600800-105626800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:105601000-105615800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:105601000-105619200	Weak transcription	GM12878-XiMat	blood
19	chr12:105601400-105615800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr12:105604200-105616200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:105604400-105618400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:105605600-105628400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:105606400-105614800	Strong transcription	Primary B cells from cord blood	blood
24	chr12:105606600-105616600	Strong transcription	Fetal Thymus	thymus
25	chr12:105606800-105617000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:105607200-105615800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:105607200-105618600	Genic enhancers	Fetal Intestine Large	intestine
28	chr12:105608200-105615600	Strong transcription	Fetal Brain Female	brain
29	chr12:105608600-105618200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:105609000-105618600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:105609200-105615200	Weak transcription	HMEC	breast
32	chr12:105609200-105620400	Genic enhancers	Fetal Intestine Small	intestine
33	chr12:105609200-105622400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:105609200-105626800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:105609200-105628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr12:105609400-105614000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:105609400-105615200	Weak transcription	HepG2	liver
38	chr12:105609400-105618600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:105609400-105619400	Strong transcription	Osteobl	bone
40	chr12:105610200-105618800	Strong transcription	Thymus	Thymus
41	chr12:105610600-105616000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:105610800-105615800	Weak transcription	Esophagus	oesophagus
43	chr12:105610800-105620000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr12:105611000-105620000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:105611000-105620200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:105611200-105620200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr12:105611200-105621200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:105611200-105628200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:105611400-105614600	Weak transcription	A549	lung
50	chr12:105611400-105615000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links