Variant report

Variant	rs6489752
Chromosome Location	chr12:942346-942347
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:940142..943103-chr12:948785..951381,2	MCF-7	breast:
2	chr12:919866..922717-chr12:940854..943432,2	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1012729	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1051669	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs1051672	0.80[EUR][1000 genomes]
rs10735063	0.81[ASN][1000 genomes]
rs10735065	1.00[ASN][1000 genomes]
rs10774459	0.81[ASN][1000 genomes]
rs10774463	0.93[ASN][1000 genomes]
rs10774466	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774468	0.95[CEU][hapmap];0.83[AMR][1000 genomes]
rs10849561	0.87[AFR][1000 genomes]
rs10849562	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849563	1.00[ASN][1000 genomes]
rs10849568	1.00[ASN][1000 genomes]
rs10849583	0.81[EUR][1000 genomes]
rs11064560	1.00[ASN][1000 genomes]
rs11064582	0.81[EUR][1000 genomes]
rs11064584	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11513723	0.81[EUR][1000 genomes]
rs11571430	0.90[CEU][hapmap];0.80[YRI][hapmap]
rs1159744	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829138	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11832907	0.95[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1970996	1.00[ASN][1000 genomes]
rs1990021	0.97[ASN][1000 genomes]
rs2014160	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2051852	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2107612	0.81[ASN][1000 genomes]
rs2107613	0.84[CEU][hapmap];0.80[ASN][1000 genomes]
rs2107614	0.93[ASN][1000 genomes]
rs2158502	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240282	1.00[ASN][1000 genomes]
rs2240283	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301880	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2369490	0.90[ASN][1000 genomes]
rs2369491	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4388955	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390400	0.86[AMR][1000 genomes]
rs4766377	0.95[CEU][hapmap]
rs4980969	1.00[ASN][1000 genomes]
rs4980970	1.00[ASN][1000 genomes]
rs4980972	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6489749	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6489751	0.97[ASN][1000 genomes]
rs6489754	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489757	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67969314	0.96[ASN][1000 genomes]
rs724709	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7298001	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300056	1.00[ASN][1000 genomes]
rs7301349	1.00[ASN][1000 genomes]
rs7309858	0.97[ASN][1000 genomes]
rs7311065	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7311423	1.00[ASN][1000 genomes]
rs765250	0.96[ASN][1000 genomes]
rs7953912	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7959921	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966632	0.93[ASN][1000 genomes]
rs7971329	1.00[ASN][1000 genomes]
rs7972490	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7980163	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 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	nsv898568	chr12:547683-969800	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv1051590	chr12:722215-974773	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv541338	chr12:722215-974773	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
15	nsv468956	chr12:737230-982321	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking 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	26 gene(s)	inside rSNPs	diseases
16	nsv556893	chr12:737230-982321	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	esv2757485	chr12:786238-964551	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
18	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
19	esv2753658	chr12:835074-964506	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
20	esv3693103	chr12:837113-971317	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
21	nsv556898	chr12:850288-968489	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
22	nsv518946	chr12:854331-961336	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
23	nsv556900	chr12:854331-968489	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
24	esv2752382	chr12:863833-964506	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	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
26	nsv898577	chr12:873890-969800	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
27	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
28	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
29	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
30	nsv522901	chr12:922408-968489	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
31	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6489752	RAD52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:905400-957000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:905400-970200	Weak transcription	Spleen	Spleen
3	chr12:914400-971000	Weak transcription	Right Ventricle	heart
4	chr12:916400-977200	Weak transcription	Gastric	stomach
5	chr12:916800-955800	Weak transcription	Stomach Mucosa	stomach
6	chr12:920200-947200	Weak transcription	Small Intestine	intestine
7	chr12:920200-966800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:921400-950200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:928000-960600	Weak transcription	Aorta	Aorta
10	chr12:928200-994400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:932800-954800	Weak transcription	Fetal Kidney	kidney
12	chr12:933400-952200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr12:933600-942800	Strong transcription	HepG2	liver
14	chr12:933600-966600	Weak transcription	Fetal Brain Female	brain
15	chr12:933600-971400	Weak transcription	Fetal Brain Male	brain
16	chr12:934000-944200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:934600-970200	Weak transcription	Colonic Mucosa	Colon
18	chr12:935000-943800	Strong transcription	Placenta	Placenta
19	chr12:935200-942600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:935200-944200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr12:935200-944600	Strong transcription	Dnd41	blood
22	chr12:935200-945000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:935800-943800	Strong transcription	Primary B cells from cord blood	blood
24	chr12:935800-944400	Weak transcription	Fetal Heart	heart
25	chr12:936000-944000	Strong transcription	HSMM	muscle
26	chr12:936000-945000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:936000-948200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr12:936200-944200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr12:936200-944400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr12:936200-944400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:936600-943600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr12:936600-944600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr12:938400-945800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:939000-960400	Weak transcription	Brain Angular Gyrus	brain
35	chr12:939200-943600	Weak transcription	Brain Anterior Caudate	brain
36	chr12:939400-944000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:939400-947200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:939400-950000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr12:939400-962800	Weak transcription	Esophagus	oesophagus
40	chr12:939600-943200	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:939600-943200	Weak transcription	Brain Substantia Nigra	brain
42	chr12:939600-943200	Weak transcription	HSMMtube	muscle
43	chr12:939600-943400	Weak transcription	Left Ventricle	heart
44	chr12:939600-943600	Weak transcription	K562	blood
45	chr12:939600-944200	Weak transcription	Psoas Muscle	Psoas
46	chr12:939600-947800	Weak transcription	Ovary	ovary
47	chr12:939600-949000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:939600-949800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr12:939600-951800	Weak transcription	Thymus	Thymus
50	chr12:939600-952200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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