Variant report

Variant	rs12231735
Chromosome Location	chr12:39726595-39726596
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	GATA3	chr12:39726501-39726891	SH-SY5Y	brain:	n/a	n/a
2	EP300	chr12:39726405-39726773	SK-N-SH_RA	brain:	n/a	chr12:39726664-39726672
3	GATA3	chr12:39726357-39726845	SK-N-SH	brain:	n/a	n/a
4	GATA2	chr12:39726403-39726964	SH-SY5Y	brain:	n/a	chr12:39726929-39726938
5	POLR2A	chr12:39726465-39726736	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr12:39726365-39726882	SK-N-SH	brain:	n/a	n/a
7	EP300	chr12:39726241-39727169	SK-N-SH	brain:	n/a	chr12:39726664-39726672
8	EP300	chr12:39726500-39726820	SK-N-SH_RA	brain:	n/a	chr12:39726664-39726672

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39725322..39729241-chr12:39730380..39734731,5	K562	blood:
2	chr12:39723120..39728244-chr12:39834929..39837982,4	MCF-7	breast:

Variant related genes	Relation type
KIF21A	TF binding region
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11171568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171662	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11171666	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171669	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11171691	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11171732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171797	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171834	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11171940	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171955	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11172168	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11172263	0.83[EUR][1000 genomes]
rs11172373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12227642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs12228664	0.83[EUR][1000 genomes]
rs12231250	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17127036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17127119	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs56154721	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56326136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56885420	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57785083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58125663	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58648215	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61101304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7964039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[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	nsv899013	chr12:39567945-39732430	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv470286	chr12:39651893-39729700	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv558589	chr12:39667861-39768356	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv558590	chr12:39724344-39751273	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39686800-39729800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:39686800-39738800	Weak transcription	Pancreas	Pancrea
3	chr12:39695600-39742000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:39696600-39762200	Weak transcription	Fetal Brain Male	brain
5	chr12:39697800-39771800	Weak transcription	Fetal Kidney	kidney
6	chr12:39699600-39760600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:39704200-39746200	Weak transcription	HUVEC	blood vessel
8	chr12:39714800-39727000	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr12:39715600-39741800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:39717800-39727400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:39718400-39756800	Weak transcription	HSMM	muscle
12	chr12:39721000-39770600	Weak transcription	Gastric	stomach
13	chr12:39721600-39734600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr12:39721600-39752400	Weak transcription	Right Ventricle	heart
15	chr12:39722000-39729000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:39722600-39737000	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:39722800-39767200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr12:39723000-39734800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:39723000-39736200	Weak transcription	NH-A	brain
20	chr12:39723400-39727000	Strong transcription	Adipose Nuclei	Adipose
21	chr12:39723400-39727200	Strong transcription	Liver	Liver
22	chr12:39723400-39727200	Strong transcription	Hela-S3	cervix
23	chr12:39723600-39735600	Weak transcription	Osteobl	bone
24	chr12:39723800-39727200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr12:39723800-39727600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:39724000-39726800	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:39724000-39726800	Strong transcription	Brain Substantia Nigra	brain
28	chr12:39724000-39726800	Strong transcription	Placenta	Placenta
29	chr12:39724000-39727000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:39724000-39727000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:39724000-39727000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:39724000-39727000	Strong transcription	Brain Anterior Caudate	brain
33	chr12:39724000-39727000	Strong transcription	Brain Germinal Matrix	brain
34	chr12:39724000-39727000	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr12:39724000-39727000	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:39724000-39727000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr12:39724000-39727000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:39724000-39727000	Strong transcription	NHEK	skin
39	chr12:39724000-39727200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:39724000-39727200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:39724200-39727000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr12:39724200-39727000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:39724200-39727000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:39724400-39727000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:39724400-39727000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:39724400-39727000	Strong transcription	GM12878-XiMat	blood
47	chr12:39724400-39727000	Strong transcription	HMEC	breast
48	chr12:39724400-39751800	Weak transcription	Fetal Heart	heart
49	chr12:39724600-39727000	Strong transcription	Brain Angular Gyrus	brain
50	chr12:39724600-39727000	Strong transcription	Esophagus	oesophagus

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