Variant report

Variant	rs4980974
Chromosome Location	chr12:985028-985029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:979797..982043-chr12:982675..985794,3	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10744729	0.83[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10849578	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10849584	0.86[ASN][1000 genomes]
rs11064580	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11064585	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11064593	0.84[ASN][1000 genomes]
rs11226	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11571409	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11571448	0.82[ASN][1000 genomes]
rs11611051	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11614499	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581940	0.92[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255390	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2269937	0.84[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286029	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3748521	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4766370	0.83[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6413436	0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7296555	0.91[ASN][1000 genomes]
rs7300444	0.83[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7300718	0.84[ASN][1000 genomes]
rs7301931	0.83[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7303748	0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7308979	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7310449	0.87[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7964502	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs953361	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541305	chr12:282465-1016828	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	esv2759875	chr12:335010-990544	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
8	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
9	esv2758290	chr12:457433-990544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv556890	chr12:662448-1100555	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS 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	58 gene(s)	inside rSNPs	diseases
11	nsv556892	chr12:673515-1210884	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
12	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised 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	56 gene(s)	inside rSNPs	diseases
13	nsv948760	chr12:863833-1542875	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised 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	42 gene(s)	inside rSNPs	diseases
14	nsv1042333	chr12:907975-1081509	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv1052589	chr12:910460-1421493	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
16	nsv1045278	chr12:920251-1697030	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
17	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
18	nsv468960	chr12:975276-1455106	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
19	nsv556941	chr12:975276-1455106	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4980974	RAD52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:928200-994400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:962200-1002600	Strong transcription	Dnd41	blood
3	chr12:962200-1012400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr12:963600-988800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:964200-1007600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:964400-1042200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:964600-1027200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:965800-1014000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:965800-1028400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:966000-985400	Strong transcription	Placenta	Placenta
11	chr12:966000-1002200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:966000-1012200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:966000-1014800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:966600-985200	Strong transcription	Liver	Liver
15	chr12:967000-988400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr12:967200-1005800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:967400-985200	Strong transcription	Osteobl	bone
18	chr12:968000-986200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:968600-1006400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:968800-993800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:970600-989000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:972200-987600	Weak transcription	Fetal Brain Male	brain
23	chr12:972200-988600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:973800-985200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:977600-987400	Weak transcription	Ovary	ovary
26	chr12:977600-988800	Weak transcription	Pancreas	Pancrea
27	chr12:977800-987200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:978000-988800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:978200-987200	Weak transcription	Brain Angular Gyrus	brain
30	chr12:978200-987400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:978200-987400	Weak transcription	NHLF	lung
32	chr12:978200-987600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:978200-988600	Weak transcription	Colonic Mucosa	Colon
34	chr12:978200-988800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:978200-988800	Weak transcription	Aorta	Aorta
36	chr12:978200-993800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr12:978400-987400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:978400-988800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:978600-987600	Weak transcription	Fetal Kidney	kidney
40	chr12:979600-985200	Strong transcription	Fetal Thymus	thymus
41	chr12:980000-986400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:980000-987200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr12:980000-988000	Weak transcription	Colon Smooth Muscle	Colon
44	chr12:980000-990600	Strong transcription	GM12878-XiMat	blood
45	chr12:980000-1013200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr12:980400-987400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:980600-987000	Weak transcription	Brain Anterior Caudate	brain
48	chr12:980600-987000	Weak transcription	Fetal Muscle Leg	muscle
49	chr12:980600-987200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr12:980600-987400	Weak transcription	Hela-S3	cervix

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