Variant report

Variant	rs7305099
Chromosome Location	chr12:975276-975277
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10744727	0.88[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs10849576	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs10849582	0.88[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs12828016	0.88[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1986231	0.88[EUR][1000 genomes]
rs2286026	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4766373	0.85[EUR][1000 genomes]
rs7303748	0.83[MKK][hapmap];0.82[YRI][hapmap]
rs7962050	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs880054	0.88[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][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	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7305099	RAD52	Cis_1M	lymphoblastoid	RTeQTL
rs7305099	CCND2	cis	parietal	SCAN
rs7305099	RAD52	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:916400-977200	Weak transcription	Gastric	stomach
2	chr12:928200-994400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:939600-977000	Weak transcription	Pancreas	Pancrea
4	chr12:960800-977200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:961000-977000	Weak transcription	Aorta	Aorta
6	chr12:961000-980200	Weak transcription	Fetal Heart	heart
7	chr12:962200-1002600	Strong transcription	Dnd41	blood
8	chr12:962200-1012400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:963600-988800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:964200-979000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr12:964200-1007600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr12:964400-1042200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:964600-1027200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:965000-980200	Weak transcription	Stomach Mucosa	stomach
15	chr12:965200-979000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:965200-983800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr12:965800-976000	Strong transcription	Primary B cells from cord blood	blood
18	chr12:965800-978600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:965800-978800	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:965800-981000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:965800-984000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:965800-984800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr12:965800-985000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:965800-1014000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr12:965800-1028400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:966000-980800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:966000-985400	Strong transcription	Placenta	Placenta
28	chr12:966000-1002200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:966000-1012200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:966000-1014800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:966200-975600	Strong transcription	Adipose Nuclei	Adipose
32	chr12:966200-978400	Strong transcription	Fetal Intestine Large	intestine
33	chr12:966600-979800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:966600-985200	Strong transcription	Liver	Liver
35	chr12:967000-988400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr12:967200-977000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:967200-978800	Strong transcription	A549	lung
38	chr12:967200-1005800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:967400-985200	Strong transcription	Osteobl	bone
40	chr12:967600-980800	Strong transcription	HSMM	muscle
41	chr12:967800-980800	Strong transcription	NHDF-Ad	bronchial
42	chr12:968000-981600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:968000-986200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:968600-1006400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:968800-978400	Strong transcription	HMEC	breast
46	chr12:968800-993800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:969000-978200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr12:969600-978400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:970600-975600	Weak transcription	Ovary	ovary
50	chr12:970600-977000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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