Variant report

Variant	rs657995
Chromosome Location	chr12:121576992-121576993
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121568948..121571142-chr12:121574770..121577289,2	MCF-7	breast:
2	chr12:121576075..121577787-chr12:121578961..121580944,2	K562	blood:
3	chr12:121575022..121577625-chr12:121581601..121583531,2	MCF-7	breast:
4	chr12:121570400..121573469-chr12:121573505..121577665,4	K562	blood:

Variant related genes	Relation type
ENSG00000089041	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10849842	0.83[ASN][1000 genomes]
rs1169714	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180009	0.88[ASN][1000 genomes]
rs12320058	0.88[ASN][1000 genomes]
rs12320178	0.83[ASN][1000 genomes]
rs1653583	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1653584	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1653585	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1718124	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1718149	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1718162	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1794886	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1794887	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1794898	0.88[ASN][1000 genomes]
rs208288	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2686369	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35646440	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3861795	0.88[ASN][1000 genomes]
rs487417	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs510660	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs511496	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs535557	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56720891	0.89[ASN][1000 genomes]
rs568531	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57263663	0.91[ASN][1000 genomes]
rs57902817	0.88[ASN][1000 genomes]
rs590477	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs592340	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs593223	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs594423	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs607094	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs608425	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs622937	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs669547	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672140	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73421546	0.91[ASN][1000 genomes]
rs73421551	0.91[ASN][1000 genomes]
rs73421553	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv430537	chr12:121487632-121579955	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv899563	chr12:121543011-121600529	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121571400-121582800	Weak transcription	Lung	lung
2	chr12:121571400-121594000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:121571600-121577200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:121571600-121579600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:121571800-121581600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:121571800-121582400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:121571800-121623200	Weak transcription	Colonic Mucosa	Colon
8	chr12:121572000-121582800	Weak transcription	Primary B cells from cord blood	blood
9	chr12:121572200-121582200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:121572200-121582400	Weak transcription	NHLF	lung
11	chr12:121572200-121583000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:121572200-121599800	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:121572600-121580000	Weak transcription	Ovary	ovary
14	chr12:121572600-121592600	Weak transcription	Liver	Liver
15	chr12:121572800-121579600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:121572800-121581400	Weak transcription	Primary B cells from peripheral blood	blood
17	chr12:121572800-121581800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:121572800-121601600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:121573400-121580000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:121574600-121577000	Strong transcription	Primary T cells from cord blood	blood
21	chr12:121574800-121577200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:121575600-121577400	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr12:121575600-121577600	Genic enhancers	Brain Hippocampus Middle	brain
24	chr12:121575600-121579000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:121575800-121577600	Genic enhancers	Brain Substantia Nigra	brain
26	chr12:121576000-121577200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr12:121576400-121577400	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr12:121576400-121577400	Enhancers	Spleen	Spleen
29	chr12:121576400-121578200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr12:121576400-121579600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr12:121576400-121579600	Weak transcription	Brain Angular Gyrus	brain
32	chr12:121576400-121580800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:121576400-121582400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:121576600-121577400	Genic enhancers	Brain Cingulate Gyrus	brain
35	chr12:121576600-121581400	Weak transcription	K562	blood
36	chr12:121576600-121581800	Weak transcription	HepG2	liver
37	chr12:121576600-121592400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:121576800-121577000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:121576800-121577200	Weak transcription	Brain Anterior Caudate	brain
40	chr12:121576800-121577400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links