Variant report

Variant	rs4980973
Chromosome Location	chr12:983046-983047
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	FOSL2	chr12:983034-983474	HepG2	liver:	n/a	n/a
2	MYBL2	chr12:982998-983425	HepG2	liver:	n/a	n/a
3	FOSL2	chr12:983017-983536	HepG2	liver:	n/a	n/a
4	FOSL2	chr12:983038-983556	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:966246..968511-chr12:980385..983217,2	K562	blood:
2	chr12:979797..982043-chr12:982675..985794,3	K562	blood:

Variant related genes	Relation type
WNK1	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10735067	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs10849603	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs11064579	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11064613	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs12231979	0.90[JPT][hapmap]
rs1833095	0.90[JPT][hapmap]
rs2887531	0.90[JPT][hapmap]
rs4766394	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs6489771	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs7294431	0.89[JPT][hapmap]
rs7311263	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs7975948	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4980973	RAD52	Cis_1M	lymphoblastoid	RTeQTL
rs4980973	RAD52	cis	cerebellum	SCAN

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	chr12:965200-983800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr12:965800-984000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:965800-984800	Strong transcription	Primary B cells from peripheral blood	blood
11	chr12:965800-985000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:965800-1014000	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:965800-1028400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:966000-985400	Strong transcription	Placenta	Placenta
15	chr12:966000-1002200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr12:966000-1012200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:966000-1014800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:966600-985200	Strong transcription	Liver	Liver
19	chr12:967000-988400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr12:967200-1005800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:967400-985200	Strong transcription	Osteobl	bone
22	chr12:968000-986200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr12:968600-1006400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:968800-993800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:970600-989000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:972200-987600	Weak transcription	Fetal Brain Male	brain
27	chr12:972200-988600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:972800-984600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:973800-985200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:975000-985000	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr12:977000-983600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:977000-983600	Strong transcription	Adipose Nuclei	Adipose
33	chr12:977000-984800	Strong transcription	Primary B cells from cord blood	blood
34	chr12:977600-987400	Weak transcription	Ovary	ovary
35	chr12:977600-988800	Weak transcription	Pancreas	Pancrea
36	chr12:977800-987200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr12:978000-983200	Weak transcription	Brain Substantia Nigra	brain
38	chr12:978000-988800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr12:978200-987200	Weak transcription	Brain Angular Gyrus	brain
40	chr12:978200-987400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr12:978200-987400	Weak transcription	NHLF	lung
42	chr12:978200-987600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:978200-988600	Weak transcription	Colonic Mucosa	Colon
44	chr12:978200-988800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:978200-988800	Weak transcription	Aorta	Aorta
46	chr12:978200-993800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr12:978400-983600	Weak transcription	K562	blood
48	chr12:978400-987400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr12:978400-988800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:978600-983200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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