Variant report

Variant	rs880054
Chromosome Location	chr12:988558-988559
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	POLR2A	chr12:988536-988576	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
WNK1	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10744727	0.88[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10849576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10849582	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12828016	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1986231	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286026	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4766373	0.89[EUR][1000 genomes]
rs7305099	0.88[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs7962050	0.95[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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
20	nsv1044329	chr12:985144-1403020	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats 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	33 gene(s)	inside rSNPs	diseases
21	nsv541340	chr12:985144-1403020	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs880054	WNK1	cis	cerebellum	SCAN
rs880054	RAD52	cis	cerebellum	SCAN
rs880054	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	chr12:966000-1002200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:966000-1012200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:966000-1014800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:967200-1005800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:968600-1006400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:968800-993800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:970600-989000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr12:972200-988600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:977600-988800	Weak transcription	Pancreas	Pancrea
19	chr12:978000-988800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:978200-988600	Weak transcription	Colonic Mucosa	Colon
21	chr12:978200-988800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:978200-988800	Weak transcription	Aorta	Aorta
23	chr12:978200-993800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:978400-988800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:980000-990600	Strong transcription	GM12878-XiMat	blood
26	chr12:980000-1013200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr12:980600-988800	Weak transcription	Stomach Mucosa	stomach
28	chr12:980600-990800	Weak transcription	Fetal Heart	heart
29	chr12:981000-988800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:981000-988800	Weak transcription	Lung	lung
31	chr12:981600-988600	Weak transcription	Fetal Stomach	stomach
32	chr12:981600-988600	Weak transcription	Gastric	stomach
33	chr12:981600-988800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:981600-988800	Weak transcription	Right Ventricle	heart
35	chr12:981600-988800	Weak transcription	Small Intestine	intestine
36	chr12:981600-988800	Weak transcription	Spleen	Spleen
37	chr12:982200-988800	Weak transcription	Psoas Muscle	Psoas
38	chr12:982200-1027000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:983600-988800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:985600-988800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:986000-996800	Strong transcription	Fetal Thymus	thymus
42	chr12:986200-1002400	Strong transcription	Left Ventricle	heart
43	chr12:986200-1042200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:986400-999800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:986400-1014800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:986600-988600	Weak transcription	Fetal Intestine Small	intestine
47	chr12:986600-999800	Strong transcription	HepG2	liver
48	chr12:986600-1012000	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:986600-1012000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:986600-1012200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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