Variant report

Variant	rs7969221
Chromosome Location	chr12:76119297-76119298
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr12:76118463-76120029	SK-N-SH	brain:	n/a	n/a
2	STAT3	chr12:76119277-76119472	MCF10A-Er-Src	breast:	n/a	chr12:76119414-76119423
3	MAX	chr12:76118508-76119775	A549	lung:	n/a	n/a
4	RAD21	chr12:76119266-76119648	Hela-S3	cervix:	n/a	n/a
5	MAX	chr12:76118327-76119848	HCT-116	colon:	n/a	n/a
6	FOS	chr12:76118501-76119606	HUVEC	blood vessel:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422
7	EP300	chr12:76118412-76119704	A549	lung:	n/a	chr12:76119415-76119424
8	FOSL2	chr12:76119198-76119623	MCF-7	breast:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422
9	SP1	chr12:76117942-76119964	HCT-116	colon:	n/a	n/a
10	EP300	chr12:76118441-76119882	ECC-1	luminal epithelium:	n/a	chr12:76119415-76119424
11	MAFK	chr12:76119236-76119616	Hela-S3	cervix:	n/a	chr12:76119422-76119442 chr12:76119425-76119439 chr12:76119424-76119440
12	NFIC	chr12:76118559-76119807	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr12:76119236-76119733	SK-N-SH_RA	brain:	n/a	chr12:76119415-76119424
14	JUND	chr12:76117952-76119857	HCT-116	colon:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422 chr12:76119739-76119748
15	MAZ	chr12:76118525-76119884	IMR90	lung:	n/a	n/a
16	PBX3	chr12:76118460-76119919	SK-N-SH	brain:	n/a	chr12:76118793-76118802
17	EP300	chr12:76118409-76119764	SK-N-SH	brain:	n/a	chr12:76119415-76119424
18	POLR2A	chr12:76119231-76119764	HCT-116	colon:	n/a	n/a
19	TEAD4	chr12:76119258-76119719	ECC-1	luminal epithelium:	n/a	n/a
20	USF2	chr12:76119272-76119613	Hela-S3	cervix:	n/a	n/a
21	RAD21	chr12:76119267-76119528	SK-N-SH_RA	brain:	n/a	n/a
22	PBX3	chr12:76118540-76119729	SK-N-SH	brain:	n/a	chr12:76118793-76118802
23	NFIC	chr12:76118367-76119767	SK-N-SH	brain:	n/a	n/a
24	CUX1	chr12:76119172-76119474	K562	blood:	n/a	n/a
25	POLR2A	chr12:76118402-76119775	PANC-1	pancreas:	n/a	n/a
26	RAD21	chr12:76119213-76119685	A549	lung:	n/a	n/a
27	RAD21	chr12:76119201-76119789	ECC-1	luminal epithelium:	n/a	n/a
28	SP1	chr12:76117868-76119975	HCT-116	colon:	n/a	n/a
29	TCF12	chr12:76118428-76119683	A549	lung:	n/a	n/a
30	FOS	chr12:76119195-76119615	MCF10A-Er-Src	breast:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422
31	RAD21	chr12:76118641-76119641	IMR90	lung:	n/a	n/a
32	TCF12	chr12:76118438-76119968	SK-N-SH	brain:	n/a	n/a
33	TCF12	chr12:76119219-76119742	ECC-1	luminal epithelium:	n/a	n/a
34	EP300	chr12:76119198-76119560	SK-N-SH_RA	brain:	n/a	chr12:76119415-76119424
35	TCF12	chr12:76118498-76119804	ECC-1	luminal epithelium:	n/a	n/a
36	GATA3	chr12:76118409-76119836	A549	lung:	n/a	chr12:76118439-76118456
37	FOSL1	chr12:76119246-76119492	K562	blood:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422
38	FOXA2	chr12:76119252-76119635	A549	lung:	n/a	n/a
39	FOS	chr12:76119213-76119619	MCF10A-Er-Src	breast:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422
40	GATA3	chr12:76118576-76119715	SK-N-SH	brain:	n/a	n/a
41	RAD21	chr12:76118179-76119905	HCT-116	colon:	n/a	n/a
42	FOXA2	chr12:76119226-76119649	A549	lung:	n/a	n/a
43	CEBPB	chr12:76119209-76119700	A549	lung:	n/a	n/a
44	JUND	chr12:76119254-76119597	Hela-S3	cervix:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422
45	POLR2A	chr12:76118723-76119683	HCT-116	colon:	n/a	n/a
46	FOSL1	chr12:76118381-76119813	HCT-116	colon:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422 chr12:76119739-76119748
47	TCF7L2	chr12:76118135-76119736	HCT-116	colon:	n/a	chr12:76119414-76119423 chr12:76118786-76118793
48	MAFK	chr12:76119236-76119611	IMR90	lung:	n/a	chr12:76119422-76119442 chr12:76119425-76119439 chr12:76119424-76119440
49	KAP1	chr12:76118601-76119659	HEK293	kidney:	n/a	chr12:76119413-76119422
50	JUND	chr12:76118105-76119932	HCT-116	colon:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422 chr12:76119739-76119748

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:76020325..76023301-chr12:76118678..76120430,2	MCF-7	breast:
2	chr12:76111051..76121376-chr12:76416110..76428653,27	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264062	TF binding region
ENSG00000139289	Chromatin interaction
ENSG00000257839	Chromatin interaction
ENSG00000257453	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11180657	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1275569	0.81[MKK][hapmap]
rs4831913	0.83[CEU][hapmap]
rs4831948	0.82[CEU][hapmap]
rs4831950	0.95[JPT][hapmap]
rs6582299	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7488278	0.82[CEU][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7969221	BBS10	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76113600-76120000	Enhancers	Fetal Stomach	stomach
2	chr12:76113600-76120200	Enhancers	Rectal Smooth Muscle	rectum
3	chr12:76114000-76119800	Enhancers	Fetal Muscle Leg	muscle
4	chr12:76114000-76120000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr12:76114200-76119800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:76114200-76120200	Enhancers	NHLF	lung
7	chr12:76114400-76119600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr12:76114400-76121200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:76114600-76120000	Enhancers	NH-A	brain
10	chr12:76114600-76120200	Enhancers	HUVEC	blood vessel
11	chr12:76115200-76120000	Enhancers	HMEC	breast
12	chr12:76115400-76121200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:76115800-76120000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:76115800-76121000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:76116600-76119400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr12:76116600-76120000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:76117200-76119400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:76118000-76119800	Enhancers	Fetal Brain Male	brain
19	chr12:76118000-76120000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:76118200-76119400	Enhancers	Small Intestine	intestine
21	chr12:76118200-76119600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr12:76118400-76119400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:76118400-76119400	Enhancers	Left Ventricle	heart
24	chr12:76118400-76119600	Enhancers	HepG2	liver
25	chr12:76118400-76119800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:76118400-76119800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:76118400-76119800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr12:76118400-76119800	Enhancers	Adipose Nuclei	Adipose
29	chr12:76118400-76119800	Enhancers	Fetal Lung	lung
30	chr12:76118400-76119800	Enhancers	K562	blood
31	chr12:76118400-76120000	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr12:76118400-76120000	Enhancers	Fetal Kidney	kidney
33	chr12:76118400-76120200	Enhancers	Colon Smooth Muscle	Colon
34	chr12:76118400-76120200	Enhancers	NHEK	skin
35	chr12:76118600-76119400	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr12:76118600-76119600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:76118600-76119600	Enhancers	Fetal Heart	heart
38	chr12:76118600-76119600	Enhancers	Stomach Smooth Muscle	stomach
39	chr12:76118600-76119800	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr12:76118600-76119800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:76118600-76119800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:76118600-76119800	Flanking Active TSS	A549	lung
43	chr12:76118600-76119800	Flanking Active TSS	NHDF-Ad	bronchial
44	chr12:76118600-76120000	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr12:76118600-76120000	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr12:76118800-76119400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:76118800-76119400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:76118800-76119400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:76118800-76119400	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr12:76118800-76119600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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