Variant report

Variant	rs11180657
Chromosome Location	chr12:76119142-76119143
allele	A/C
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	MAX	chr12:76118508-76119775	A549	lung:	n/a	n/a
3	MAX	chr12:76118327-76119848	HCT-116	colon:	n/a	n/a
4	FOS	chr12:76118501-76119606	HUVEC	blood vessel:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422
5	EP300	chr12:76118412-76119704	A549	lung:	n/a	chr12:76119415-76119424
6	SP1	chr12:76117942-76119964	HCT-116	colon:	n/a	n/a
7	EP300	chr12:76118441-76119882	ECC-1	luminal epithelium:	n/a	chr12:76119415-76119424
8	NFIC	chr12:76118559-76119807	ECC-1	luminal epithelium:	n/a	n/a
9	JUND	chr12:76117952-76119857	HCT-116	colon:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422 chr12:76119739-76119748
10	MAZ	chr12:76118525-76119884	IMR90	lung:	n/a	n/a
11	PBX3	chr12:76118460-76119919	SK-N-SH	brain:	n/a	chr12:76118793-76118802
12	EP300	chr12:76118409-76119764	SK-N-SH	brain:	n/a	chr12:76119415-76119424
13	EP300	chr12:76118532-76119166	A549	lung:	n/a	n/a
14	PBX3	chr12:76118540-76119729	SK-N-SH	brain:	n/a	chr12:76118793-76118802
15	NFIC	chr12:76118367-76119767	SK-N-SH	brain:	n/a	n/a
16	SIN3AK20	chr12:76118696-76119195	A549	lung:	n/a	n/a
17	POLR2A	chr12:76118402-76119775	PANC-1	pancreas:	n/a	n/a
18	JUND	chr12:76118484-76119215	T-47D	breast:	n/a	n/a
19	SP1	chr12:76117868-76119975	HCT-116	colon:	n/a	n/a
20	TCF12	chr12:76118428-76119683	A549	lung:	n/a	n/a
21	RAD21	chr12:76118641-76119641	IMR90	lung:	n/a	n/a
22	TCF12	chr12:76118438-76119968	SK-N-SH	brain:	n/a	n/a
23	TCF12	chr12:76118498-76119804	ECC-1	luminal epithelium:	n/a	n/a
24	GATA3	chr12:76118409-76119836	A549	lung:	n/a	chr12:76118439-76118456
25	GATA3	chr12:76118576-76119715	SK-N-SH	brain:	n/a	n/a
26	RAD21	chr12:76118179-76119905	HCT-116	colon:	n/a	n/a
27	POLR2A	chr12:76118723-76119683	HCT-116	colon:	n/a	n/a
28	FOSL1	chr12:76118381-76119813	HCT-116	colon:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422 chr12:76119739-76119748
29	TCF7L2	chr12:76118135-76119736	HCT-116	colon:	n/a	chr12:76119414-76119423 chr12:76118786-76118793
30	KAP1	chr12:76118601-76119659	HEK293	kidney:	n/a	chr12:76119413-76119422
31	JUND	chr12:76118105-76119932	HCT-116	colon:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422 chr12:76119739-76119748
32	CBX3	chr12:76118161-76119839	HCT-116	colon:	n/a	n/a
33	BCL3	chr12:76118567-76119418	A549	lung:	n/a	n/a
34	SP1	chr12:76118337-76119743	A549	lung:	n/a	n/a
35	NFIC	chr12:76118547-76119733	ECC-1	luminal epithelium:	n/a	n/a
36	GATA3	chr12:76118415-76119780	SK-N-SH	brain:	n/a	chr12:76118439-76118456
37	POLR2A	chr12:76118498-76119143	HUVEC	blood vessel:	n/a	n/a
38	JUND	chr12:76118527-76119737	SK-N-SH	brain:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422
39	POLR2A	chr12:76118688-76119158	HCT-116	colon:	n/a	n/a
40	FOSL2	chr12:76118477-76119784	SK-N-SH	brain:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422 chr12:76119739-76119748
41	FOSL2	chr12:76118304-76119795	A549	lung:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422 chr12:76119739-76119748
42	MAX	chr12:76118615-76119676	A549	lung:	n/a	n/a
43	FOXA2	chr12:76118711-76119169	A549	lung:	n/a	n/a
44	POLR2A	chr12:76117997-76120227	HCT-116	colon:	n/a	n/a
45	FOSL1	chr12:76118195-76119907	HCT-116	colon:	n/a	chr12:76119415-76119424 chr12:76119414-76119424 chr12:76119414-76119424 chr12:76119415-76119422 chr12:76119739-76119748
46	SP1	chr12:76118512-76119620	A549	lung:	n/a	n/a
47	FOXM1	chr12:76119073-76119859	ECC-1	luminal epithelium:	n/a	n/a
48	TEAD4	chr12:76118463-76119169	A549	lung:	n/a	chr12:76118751-76118760
49	TCF7L2	chr12:76118457-76119675	PANC-1	pancreas:	n/a	chr12:76119414-76119423 chr12:76118786-76118793
50	MEF2A	chr12:76118499-76119540	SK-N-SH	brain:	n/a	n/a

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
ENSG00000257453	Chromatin interaction
ENSG00000257839	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1275569	0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1493788	0.89[AFR][1000 genomes]
rs4831913	0.83[CEU][hapmap]
rs4831948	0.82[CEU][hapmap]
rs4831950	0.95[JPT][hapmap]
rs6582299	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7306470	0.92[AFR][1000 genomes]
rs7488278	0.83[ASW][hapmap];0.82[CEU][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7969221	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]

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
rs11180657	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	chr12:76114200-76119200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:76114200-76119800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:76114200-76120200	Enhancers	NHLF	lung
8	chr12:76114400-76119600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr12:76114400-76121200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:76114600-76120000	Enhancers	NH-A	brain
11	chr12:76114600-76120200	Enhancers	HUVEC	blood vessel
12	chr12:76115200-76120000	Enhancers	HMEC	breast
13	chr12:76115400-76121200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:76115800-76120000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:76115800-76121000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:76116600-76119400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:76116600-76120000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:76117200-76119400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:76117600-76119200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:76118000-76119800	Enhancers	Fetal Brain Male	brain
21	chr12:76118000-76120000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:76118200-76119400	Enhancers	Small Intestine	intestine
23	chr12:76118200-76119600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr12:76118400-76119400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:76118400-76119400	Enhancers	Left Ventricle	heart
26	chr12:76118400-76119600	Enhancers	HepG2	liver
27	chr12:76118400-76119800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:76118400-76119800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:76118400-76119800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr12:76118400-76119800	Enhancers	Adipose Nuclei	Adipose
31	chr12:76118400-76119800	Enhancers	Fetal Lung	lung
32	chr12:76118400-76119800	Enhancers	K562	blood
33	chr12:76118400-76120000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr12:76118400-76120000	Enhancers	Fetal Kidney	kidney
35	chr12:76118400-76120200	Enhancers	Colon Smooth Muscle	Colon
36	chr12:76118400-76120200	Enhancers	NHEK	skin
37	chr12:76118600-76119200	Flanking Active TSS	HSMMtube	muscle
38	chr12:76118600-76119400	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr12:76118600-76119600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:76118600-76119600	Enhancers	Fetal Heart	heart
41	chr12:76118600-76119600	Enhancers	Stomach Smooth Muscle	stomach
42	chr12:76118600-76119800	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr12:76118600-76119800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:76118600-76119800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:76118600-76119800	Flanking Active TSS	A549	lung
46	chr12:76118600-76119800	Flanking Active TSS	NHDF-Ad	bronchial
47	chr12:76118600-76120000	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr12:76118600-76120000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr12:76118800-76119200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:76118800-76119200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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