Variant report

Variant	rs4390400
Chromosome Location	chr12:1002846-1002847
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	chr12:1000108..1002926-chr12:1003679..1005359,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1012729	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1051669	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1051672	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10774466	0.86[AMR][1000 genomes]
rs10774468	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10849583	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11064582	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11064584	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11513723	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11571430	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11829138	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11832907	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051852	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158502	0.86[AMR][1000 genomes]
rs2301880	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2369491	0.86[AMR][1000 genomes]
rs4388955	0.86[AMR][1000 genomes]
rs4766377	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6489752	0.86[AMR][1000 genomes]
rs724709	0.85[AMR][1000 genomes]
rs7298001	0.86[AMR][1000 genomes]
rs7305042	0.83[EUR][1000 genomes]
rs7953912	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7959921	0.86[AMR][1000 genomes]
rs7972490	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	nsv1053198	chr12:993822-1034603	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
21	nsv541341	chr12:993822-1034603	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
22	nsv1041675	chr12:993822-1091354	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
23	nsv470256	chr12:998365-1438761	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	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
rs4390400	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	chr12:962200-1012400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr12:964200-1007600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr12:964400-1042200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:964600-1027200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr12:965800-1014000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:965800-1028400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:966000-1012200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:966000-1014800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:967200-1005800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:968600-1006400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:980000-1013200	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr12:982200-1027000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:986200-1042200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:986400-1014800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:986600-1012000	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr12:986600-1012000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:986600-1012200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:986800-1014600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr12:986800-1028400	Strong transcription	Placenta	Placenta
20	chr12:987000-1007000	Strong transcription	HUVEC	blood vessel
21	chr12:987000-1007200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
22	chr12:987000-1011200	Strong transcription	Liver	Liver
23	chr12:987000-1012600	Strong transcription	Primary T cells from cord blood	blood
24	chr12:987000-1014800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr12:987000-1017600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:987000-1020800	Strong transcription	Adipose Nuclei	Adipose
27	chr12:987000-1022400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:987000-1023600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:987000-1028400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:987000-1028800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:987000-1041200	Strong transcription	Fetal Intestine Large	intestine
32	chr12:987200-1005400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:987200-1024400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:987200-1024400	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr12:987400-1007400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr12:988600-1029400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr12:988800-1023600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr12:989200-1005400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:989200-1006600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:989200-1042200	Strong transcription	Fetal Muscle Leg	muscle
41	chr12:989400-1005000	Strong transcription	Osteobl	bone
42	chr12:989400-1006200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:989400-1012800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:989400-1028400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:990000-1006400	Strong transcription	HSMM	muscle
46	chr12:994400-1005600	Weak transcription	Psoas Muscle	Psoas
47	chr12:994800-1005200	Weak transcription	Small Intestine	intestine
48	chr12:995200-1004800	Weak transcription	Esophagus	oesophagus
49	chr12:995200-1004800	Weak transcription	Gastric	stomach
50	chr12:995200-1005200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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