Variant report

Variant	rs2160589
Chromosome Location	chr12:12379293-12379294
allele	C/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	KAP1	chr12:12379091-12379567	HEK293	kidney:	n/a	n/a
2	SETDB1	chr12:12378987-12379702	U2OS	brain:	n/a	n/a
3	STAT3	chr12:12379293-12379330	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12378227..12379810-chr12:12418939..12421766,2	K562	blood:

Variant related genes	Relation type
RNU6-545P	TF binding region
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10431232	0.92[EUR][1000 genomes]
rs10431303	0.92[EUR][1000 genomes]
rs10743981	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1074992	0.87[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs1074993	0.92[EUR][1000 genomes]
rs10772544	0.89[EUR][1000 genomes]
rs10845498	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10845504	0.86[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs10845505	0.86[EUR][1000 genomes]
rs11054697	0.81[EUR][1000 genomes]
rs11054701	0.92[ASW][hapmap];0.93[CEU][hapmap];0.89[GIH][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11054752	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1181333	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1468878	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1548958	0.92[EUR][1000 genomes]
rs16907786	0.84[ASW][hapmap];0.93[CEU][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16907810	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2075241	0.92[CEU][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs2160521	0.85[EUR][1000 genomes]
rs2300231	0.92[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2417090	0.89[EUR][1000 genomes]
rs3825258	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs4265667	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4494380	0.89[EUR][1000 genomes]
rs4619236	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs4763789	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61130413	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7134001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7136380	0.87[EUR][1000 genomes]
rs7295656	0.92[EUR][1000 genomes]
rs7310538	0.90[EUR][1000 genomes]
rs7311987	0.89[EUR][1000 genomes]
rs7313285	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968660	0.87[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2160589	MANSC1	cis	parietal	SCAN
rs2160589	LRP6	cis	cerebellum	SCAN
rs2160589	M6PR	cis	cerebellum	SCAN
rs2160589	DERA	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
2	chr12:12368200-12381400	Weak transcription	Gastric	stomach
3	chr12:12368200-12384200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:12368600-12381000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:12368600-12381400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:12370600-12380800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:12370600-12381000	Weak transcription	Left Ventricle	heart
9	chr12:12370800-12380800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:12370800-12392200	Weak transcription	Brain Substantia Nigra	brain
11	chr12:12373000-12380800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:12373000-12381200	Weak transcription	Lung	lung
13	chr12:12374600-12381000	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:12374600-12381400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:12374800-12380600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:12374800-12380600	Weak transcription	Brain Angular Gyrus	brain
17	chr12:12374800-12380800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:12374800-12383200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr12:12375000-12380800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:12375200-12379400	Weak transcription	Fetal Kidney	kidney
21	chr12:12376800-12380000	Enhancers	HepG2	liver
22	chr12:12377200-12381000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:12377200-12381200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:12377400-12382400	Weak transcription	HSMM	muscle
25	chr12:12377800-12384200	Weak transcription	K562	blood
26	chr12:12377800-12407200	Weak transcription	NH-A	brain
27	chr12:12378800-12379400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:12378800-12380800	ZNF genes & repeats	A549	lung
29	chr12:12379000-12379400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
30	chr12:12379000-12379600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:12379000-12379800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:12379200-12379400	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr12:12379200-12380200	Enhancers	Liver	Liver
34	chr12:12379200-12396800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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