Variant report

Variant	rs10161536
Chromosome Location	chr12:46277726-46277727
allele	C/T
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	POLR2A	chr12:46277700-46277756	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:46122283..46124840-chr12:46276050..46278678,3	MCF-7	breast:
2	chr12:46121036..46122652-chr12:46277121..46278635,2	K562	blood:
3	chr12:46273812..46279067-chr12:46282105..46286818,5	K562	blood:
4	chr12:46122767..46124375-chr12:46276230..46278383,2	K562	blood:

Variant related genes	Relation type
KNOP1P2	TF binding region
ENSG00000189079	Chromatin interaction
ENSG00000273015	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10161001	0.90[AFR][1000 genomes]
rs10161062	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10161510	1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[YRI][hapmap]
rs10506264	0.93[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10880858	1.00[YRI][hapmap]
rs11183248	0.93[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574971	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12296933	1.00[YRI][hapmap]
rs12297214	0.83[YRI][hapmap]
rs12298184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12302862	0.80[YRI][hapmap]
rs12307979	0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12309988	0.91[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12314576	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1549591	1.00[EUR][1000 genomes]
rs15852	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17096316	1.00[EUR][1000 genomes]
rs61009645	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6582575	0.91[ASW][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap]
rs6582580	1.00[EUR][1000 genomes]
rs7133123	1.00[YRI][hapmap]
rs7296694	0.91[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs7303119	1.00[CHD][hapmap];0.86[YRI][hapmap]
rs7304785	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7306774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7308856	1.00[CHD][hapmap];0.80[YRI][hapmap]
rs7308893	0.91[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap]
rs7310702	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74081279	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74081280	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74081611	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7964495	1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[YRI][hapmap]
rs7965539	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7970212	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7970367	1.00[EUR][1000 genomes]
rs7971936	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7972499	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7972650	1.00[CHD][hapmap];0.85[YRI][hapmap]
rs7973967	0.86[YRI][hapmap]
rs7975170	1.00[CHD][hapmap];0.80[YRI][hapmap]
rs7975408	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832396	chr12:46155424-46310583	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv558782	chr12:46254995-46286683	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46245400-46318600	Weak transcription	Small Intestine	intestine
2	chr12:46246000-46285400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:46246600-46285400	Weak transcription	NH-A	brain
4	chr12:46246600-46285600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:46246600-46286000	Weak transcription	HMEC	breast
6	chr12:46246800-46288000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:46248000-46279400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:46248000-46279600	Weak transcription	Gastric	stomach
9	chr12:46251800-46283400	Strong transcription	Fetal Thymus	thymus
10	chr12:46254800-46278600	Weak transcription	NHEK	skin
11	chr12:46259000-46316600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:46262200-46278400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr12:46269000-46279400	Weak transcription	Pancreas	Pancrea
14	chr12:46269000-46287000	Weak transcription	Esophagus	oesophagus
15	chr12:46269000-46319200	Weak transcription	Spleen	Spleen
16	chr12:46269200-46289000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:46269400-46316200	Weak transcription	Brain Angular Gyrus	brain
18	chr12:46269600-46278600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:46269600-46285600	Weak transcription	HSMM	muscle
20	chr12:46269600-46285600	Weak transcription	HSMMtube	muscle
21	chr12:46269600-46285800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr12:46269600-46287800	Weak transcription	Colonic Mucosa	Colon
23	chr12:46269800-46279000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:46269800-46285800	Weak transcription	Fetal Kidney	kidney
25	chr12:46269800-46285800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr12:46269800-46285800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr12:46269800-46315800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr12:46270000-46279200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:46270000-46279200	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:46270000-46287200	Weak transcription	Osteobl	bone
31	chr12:46270200-46278400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr12:46270200-46279400	Weak transcription	Left Ventricle	heart
33	chr12:46270200-46285800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:46270600-46279200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:46271200-46278400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:46271200-46279400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:46271200-46285400	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:46271200-46285600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr12:46271400-46285800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr12:46271800-46278800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:46272400-46277800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:46272800-46285600	Weak transcription	HUVEC	blood vessel
43	chr12:46273000-46281200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr12:46273400-46285600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr12:46273400-46307600	Weak transcription	NHLF	lung
46	chr12:46273400-46310200	Weak transcription	Stomach Mucosa	stomach
47	chr12:46273400-46311200	Weak transcription	Right Ventricle	heart
48	chr12:46273400-46314400	Weak transcription	Brain Substantia Nigra	brain
49	chr12:46273600-46286000	Weak transcription	Brain Anterior Caudate	brain
50	chr12:46273800-46278600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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