Variant report

Variant	rs6489749
Chromosome Location	chr12:896965-896966
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	chr12:881327..883755-chr12:895131..898641,3	K562	blood:
2	chr12:881327..884915-chr12:893641..898608,4	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10735063	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10735064	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10735065	0.93[ASN][1000 genomes]
rs10774459	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10774463	1.00[ASN][1000 genomes]
rs10774466	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10849562	0.85[ASN][1000 genomes]
rs10849563	0.93[ASN][1000 genomes]
rs10849568	0.93[ASN][1000 genomes]
rs11064560	0.93[ASN][1000 genomes]
rs1159744	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1970996	0.93[ASN][1000 genomes]
rs1990021	0.90[ASN][1000 genomes]
rs2014160	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2107612	0.88[ASN][1000 genomes]
rs2107613	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2107614	1.00[ASN][1000 genomes]
rs2158502	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2240282	0.93[ASN][1000 genomes]
rs2240283	0.93[ASN][1000 genomes]
rs2369402	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2369490	0.97[ASN][1000 genomes]
rs2369491	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4388955	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4980968	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4980969	0.93[ASN][1000 genomes]
rs4980970	0.93[ASN][1000 genomes]
rs4980972	0.91[ASN][1000 genomes]
rs6489751	0.90[ASN][1000 genomes]
rs6489752	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6489754	0.93[ASN][1000 genomes]
rs6489757	0.93[ASN][1000 genomes]
rs67969314	0.97[ASN][1000 genomes]
rs724709	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295704	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7298001	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7300056	0.93[ASN][1000 genomes]
rs7301349	0.93[ASN][1000 genomes]
rs7309858	0.90[ASN][1000 genomes]
rs7311065	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311423	0.93[ASN][1000 genomes]
rs765250	0.97[ASN][1000 genomes]
rs7959921	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7966632	1.00[ASN][1000 genomes]
rs7971329	0.93[ASN][1000 genomes]
rs7980163	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 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	nsv1046707	chr12:792110-910520	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	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
20	esv2754685	chr12:835074-936468	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
21	esv2753750	chr12:835074-939480	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
22	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
23	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
24	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
25	nsv468959	chr12:850613-922408	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
26	nsv556899	chr12:850613-922408	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
27	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
28	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
29	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
30	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
31	esv1840640	chr12:866857-898400	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
32	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
33	nsv898578	chr12:876288-909731	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
34	nsv524544	chr12:889902-922408	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6489749	RAD52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:883600-905200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:883800-923200	Weak transcription	Fetal Stomach	stomach
3	chr12:884800-899000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:885400-897000	Weak transcription	Fetal Intestine Small	intestine
5	chr12:885400-898400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:885400-904000	Weak transcription	Thymus	Thymus
7	chr12:889000-897600	Weak transcription	Fetal Intestine Large	intestine
8	chr12:889000-898800	Weak transcription	Psoas Muscle	Psoas
9	chr12:889000-899600	Weak transcription	Primary B cells from cord blood	blood
10	chr12:889000-904000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:889000-907000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:889200-898800	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr12:889400-927600	Weak transcription	Aorta	Aorta
14	chr12:889600-898200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:889800-898800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:890000-897000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:890000-898200	Weak transcription	Stomach Mucosa	stomach
18	chr12:890200-897000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:890400-898200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr12:890400-898400	Weak transcription	NHLF	lung
21	chr12:890400-898600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:890400-898800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr12:890400-899000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:890400-899000	Weak transcription	Fetal Lung	lung
25	chr12:890600-898000	Weak transcription	Brain Angular Gyrus	brain
26	chr12:890600-898200	Weak transcription	NHEK	skin
27	chr12:890600-898600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:891400-897000	Weak transcription	Hela-S3	cervix
29	chr12:891400-899000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:891600-897200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:891600-897200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr12:891600-897200	Weak transcription	Osteobl	bone
33	chr12:891600-902200	Weak transcription	HSMM	muscle
34	chr12:892200-898200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:892400-904000	Weak transcription	Fetal Thymus	thymus
36	chr12:892400-905000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:892800-898800	Weak transcription	Ovary	ovary
38	chr12:893400-907400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:894000-898000	Weak transcription	Brain Substantia Nigra	brain
40	chr12:894400-904000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:894800-897400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:894800-901400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr12:895000-897400	Enhancers	Right Atrium	heart
44	chr12:895000-902600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr12:895000-903400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr12:895000-905400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr12:895200-897200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr12:895200-897800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:895400-897000	Enhancers	Brain Cingulate Gyrus	brain
50	chr12:895400-898800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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