Variant report

Variant	rs11065230
Chromosome Location	chr12:121164652-121164653
allele	C/T
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:7)
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	POLR2A	chr12:121164615-121164807	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:121164646-121164696	AG09309	skin:	n/a
2	chr12:121164646-121164696	MCF-7	breast:	n/a
3	chr12:121164646-121164696	Jurkat	blood:	n/a
4	chr12:121164646-121164696	Hepatocyte	liver:	n/a
5	chr12:121164646-121164696	AG04450	lung:	fetal
6	chr12:121164646-121164696	NHBE	bronchial:	n/a
7	chr12:121164646-121164696	IMR90	lung:	fetal
8	chr12:121164646-121164696	SAEC	small airway:	n/a
9	chr12:121164646-121164696	HCT-116	colon:	n/a
10	chr12:121164646-121164696	GM19239	blood:	n/a
11	chr12:121164646-121164696	CMK	blood:	n/a
12	chr12:121164646-121164696	U87	brain:	n/a
13	chr12:121164646-121164696	A549	lung:	n/a
14	chr12:121164646-121164696	HCF	heart:	n/a
15	chr12:121164646-121164696	HRPEpiC	eye:	n/a
16	chr12:121164646-121164696	HAEpiC	amniotic membrane:	n/a
17	chr12:121164646-121164696	SK-N-SH_RA	brain:	n/a
18	chr12:121164646-121164696	HL-60	blood:	n/a
19	chr12:121164646-121164696	HCM	heart:	n/a
20	chr12:121164646-121164696	PANC-1	pancreas:	n/a
21	chr12:121164646-121164696	LNCaP	prostate:	n/a
22	chr12:121164646-121164696	ProgFib	skin:	n/a
23	chr12:121164646-121164696	AG09319	gingival:	n/a
24	chr12:121164646-121164696	T-47D	breast:	n/a
25	chr12:121164646-121164696	NHDF-neo	bronchial:	n/a
26	chr12:121164646-121164696	K562	blood:	n/a
27	chr12:121164646-121164696	SK-N-SH	brain:	n/a
28	chr12:121164646-121164696	BE2_C	brain:	n/a
29	chr12:121164646-121164696	AG04449	skin:	fetal
30	chr12:121164646-121164696	HIPEpiC	eye:	n/a
31	chr12:121164646-121164696	AoSMC	blood vessel:	n/a
32	chr12:121164646-121164696	PrEC	prostate:	n/a
33	chr12:121164646-121164696	HEK293	kidney:	embryo
34	chr12:121164646-121164696	GM12878	blood:	n/a
35	chr12:121164646-121164696	SKMC	muscle:	n/a
36	chr12:121164646-121164696	NB4	blood:	n/a
37	chr12:121164646-121164696	AG10803	skin:	n/a
38	chr12:121164646-121164696	ovcar-3	ovarian:	n/a
39	chr12:121164646-121164696	HMEC	breast:	n/a
40	chr12:121164646-121164696	BJ	skin:	n/a
41	chr12:121164646-121164696	HRE	kidney:	n/a
42	chr12:121164646-121164696	HNPCEpiC	eye:	n/a
43	chr12:121164646-121164696	HUVEC	blood vessel:	n/a
44	chr12:121164646-121164696	HCPEpiC	choroid plexus:	n/a
45	chr12:121164646-121164696	HRCEpiC	kidney:	n/a
46	chr12:121164646-121164696	Caco-2	colon:	n/a
47	chr12:121164646-121164696	GM06990	blood:	n/a
48	chr12:121164646-121164696	PFSK-1	brain:	n/a
49	chr12:121164646-121164696	Hela-S3	cervix:	n/a
50	chr12:121164646-121164696	NH-A	brain:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121157650..121161198-chr12:121163529..121166472,5	K562	blood:
2	chr12:121018631..121020878-chr12:121162530..121164769,2	MCF-7	breast:
3	chr12:121163485..121165709-chr12:121272071..121274503,2	MCF-7	breast:
4	chr12:120932256..120933907-chr12:121163568..121165068,2	K562	blood:
5	chr12:121146305..121152610-chr12:121160959..121168394,8	MCF-7	breast:
6	chr12:121164614..121167510-chr12:121171430..121173002,2	K562	blood:
7	chr12:120729060..120730758-chr12:121163308..121164812,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000256569	TF binding region
ENSG00000256569	CpG island
ENSG00000175970	Chromatin interaction
ENSG00000167272	Chromatin interaction
ENSG00000088986	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000157837	Chromatin interaction
ENSG00000248008	Chromatin interaction
ENSG00000265455	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10849779	0.93[ASN][1000 genomes]
rs11065208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11065211	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065212	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065270	0.85[JPT][hapmap]
rs11065314	0.85[JPT][hapmap]
rs11829037	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833718	0.89[JPT][hapmap]
rs12296423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12306138	0.85[JPT][hapmap]
rs1533810	0.86[JPT][hapmap]
rs1803508	0.96[ASN][1000 genomes]
rs3830155	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559761	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55644516	0.89[EUR][1000 genomes]
rs59358833	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59904018	0.89[EUR][1000 genomes]
rs61229807	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489783	0.85[JPT][hapmap]
rs6490302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs695950	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7133413	0.85[JPT][hapmap]
rs7135915	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7303170	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307973	0.85[JPT][hapmap]
rs7309538	0.86[JPT][hapmap]
rs7313532	0.89[JPT][hapmap]
rs73409923	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7956685	0.89[EUR][1000 genomes]
rs7958698	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7960336	0.86[JPT][hapmap]
rs7964228	0.91[ASN][1000 genomes]
rs7972583	0.97[ASN][1000 genomes]
rs7972912	0.85[JPT][hapmap]
rs7973907	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs949443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv899558	chr12:121161589-121179939	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121163000-121165000	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr12:121163400-121164800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:121163400-121165200	Active TSS	Rectal Smooth Muscle	rectum
4	chr12:121163600-121164800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:121164000-121164800	Flanking Active TSS	Dnd41	blood
6	chr12:121164000-121165200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
7	chr12:121164000-121165600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:121164000-121177000	Weak transcription	Aorta	Aorta
9	chr12:121164200-121164800	Enhancers	Brain Substantia Nigra	brain
10	chr12:121164200-121164800	Enhancers	Fetal Thymus	thymus
11	chr12:121164200-121164800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr12:121164200-121164800	Flanking Active TSS	HepG2	liver
13	chr12:121164200-121165000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:121164200-121165000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:121164200-121165000	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr12:121164200-121165000	Enhancers	Spleen	Spleen
17	chr12:121164200-121165400	Flanking Active TSS	Liver	Liver
18	chr12:121164200-121167200	Weak transcription	Ovary	ovary
19	chr12:121164200-121167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:121164200-121167400	Weak transcription	Brain Germinal Matrix	brain
21	chr12:121164200-121169800	Weak transcription	NH-A	brain
22	chr12:121164200-121170800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:121164200-121172600	Weak transcription	HSMMtube	muscle
24	chr12:121164200-121176400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:121164400-121164800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:121164400-121164800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:121164400-121164800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:121164400-121164800	Active TSS	Primary hematopoietic stem cells	blood
29	chr12:121164400-121164800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr12:121164400-121164800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr12:121164400-121164800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:121164400-121164800	Weak transcription	Brain Anterior Caudate	brain
33	chr12:121164400-121164800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr12:121164400-121164800	Enhancers	Fetal Muscle Leg	muscle
35	chr12:121164400-121164800	Weak transcription	Fetal Stomach	stomach
36	chr12:121164400-121164800	Flanking Active TSS	Psoas Muscle	Psoas
37	chr12:121164400-121164800	Weak transcription	Thymus	Thymus
38	chr12:121164400-121165000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:121164400-121165000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:121164400-121165000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:121164400-121165000	Enhancers	Lung	lung
42	chr12:121164400-121165200	Enhancers	Primary T cells fromperipheralblood	blood
43	chr12:121164400-121165600	Enhancers	Stomach Mucosa	stomach
44	chr12:121164400-121165800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:121164400-121165800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:121164400-121166200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:121164400-121166600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:121164400-121167600	Weak transcription	Fetal Lung	lung
49	chr12:121164400-121168000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:121164400-121168200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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