Variant report

Variant	rs10849559
Chromosome Location	chr12:916310-916311
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	chr12:861876..864067-chr12:916033..918768,2	MCF-7	breast:
2	chr12:860752..862615-chr12:913879..916697,2	K562	blood:

Variant related genes	Relation type
ENSG00000060237	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10774464	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10774465	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10774467	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10849557	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10849560	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10849561	0.97[ASN][1000 genomes]
rs10849563	0.86[JPT][hapmap]
rs10849564	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11064543	0.81[ASN][1000 genomes]
rs11064560	0.86[JPT][hapmap]
rs11064575	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1159744	0.86[JPT][hapmap]
rs11608756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11615237	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2107612	0.86[JPT][hapmap]
rs2107613	0.86[JPT][hapmap]
rs2158501	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2158502	0.86[JPT][hapmap]
rs2240284	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2369402	0.86[JPT][hapmap]
rs6489756	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7137311	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs727880	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7298426	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7305065	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7311290	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7311746	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7314017	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs765250	0.86[JPT][hapmap]
rs7959509	0.83[ASN][1000 genomes]
rs7963376	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 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	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	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
31	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
32	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
33	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10849559	RAD52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:883800-923200	Weak transcription	Fetal Stomach	stomach
2	chr12:889400-927600	Weak transcription	Aorta	Aorta
3	chr12:899600-939200	Weak transcription	Pancreas	Pancrea
4	chr12:902400-924200	Weak transcription	HMEC	breast
5	chr12:904600-919600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:905200-919600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:905400-920000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:905400-939200	Weak transcription	Esophagus	oesophagus
9	chr12:905400-957000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:905400-970200	Weak transcription	Spleen	Spleen
11	chr12:909400-923800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:909600-918000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:910000-919600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:910000-919800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:910800-933000	Weak transcription	Right Atrium	heart
16	chr12:911600-919800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:912000-919800	Weak transcription	NHEK	skin
18	chr12:912000-922600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:912000-923600	Weak transcription	Fetal Lung	lung
20	chr12:912400-916400	Weak transcription	Fetal Kidney	kidney
21	chr12:912600-919600	Weak transcription	HSMM	muscle
22	chr12:913000-923400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr12:913000-923400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr12:913000-939000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:913200-916800	Enhancers	Fetal Heart	heart
26	chr12:913400-922000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr12:913600-917000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr12:913600-936000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr12:913800-916600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:913800-917800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:913800-921200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:914000-916800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:914200-916800	Enhancers	Brain Substantia Nigra	brain
34	chr12:914200-918800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr12:914400-916600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:914400-916800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr12:914400-916800	Flanking Active TSS	GM12878-XiMat	blood
38	chr12:914400-918000	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr12:914400-919800	Weak transcription	Ovary	ovary
40	chr12:914400-971000	Weak transcription	Right Ventricle	heart
41	chr12:914600-916800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:914600-919200	Weak transcription	Brain Angular Gyrus	brain
43	chr12:914600-919800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:914600-919800	Weak transcription	K562	blood
45	chr12:914600-923600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:915000-916800	Enhancers	NHDF-Ad	bronchial
47	chr12:915000-916800	Enhancers	Osteobl	bone
48	chr12:915000-917800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr12:915200-916400	Enhancers	Fetal Intestine Large	intestine
50	chr12:915200-916400	Flanking Active TSS	A549	lung

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