Variant report

Variant	rs13302964
Chromosome Location	chr12:11307496-11307497
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11305963..11307778-chr12:11320595..11323061,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11516172	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11522335	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1451767	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28542794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34263586	0.86[EUR][1000 genomes]
rs34280471	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34315443	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34423519	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34490574	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34808476	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34825996	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34897085	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34989493	0.85[EUR][1000 genomes]
rs35034090	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs35039890	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs35641223	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs35760416	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35860793	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs35962483	0.86[EUR][1000 genomes]
rs36057066	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3851591	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7135943	0.86[EUR][1000 genomes]
rs7296803	0.85[AFR][1000 genomes]
rs7299875	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73051374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7959172	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7970990	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7980237	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758294	chr12:10969620-11714921	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription 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	52 gene(s)	inside rSNPs	diseases
2	esv2759879	chr12:10969620-11714921	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS 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	52 gene(s)	inside rSNPs	diseases
3	nsv1038277	chr12:11060978-11504091	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv428272	chr12:11069845-11714921	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv898783	chr12:11185236-11338781	ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv898784	chr12:11188140-11341521	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS 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	25 gene(s)	inside rSNPs	diseases
7	nsv1050050	chr12:11192046-11436359	Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv1053783	chr12:11203509-11495584	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	esv1807067	chr12:11214215-11568895	Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription 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	33 gene(s)	inside rSNPs	diseases
10	nsv1042134	chr12:11220712-11328131	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv1043344	chr12:11220827-11308162	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13302964	PRR4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11262200-11314600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:11262800-11318200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:11268600-11312600	Weak transcription	Hela-S3	cervix
4	chr12:11270400-11323200	Weak transcription	Fetal Kidney	kidney
5	chr12:11273800-11321800	Weak transcription	Osteobl	bone
6	chr12:11276800-11311800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:11279400-11311800	Weak transcription	HepG2	liver
8	chr12:11282400-11318200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr12:11286600-11318600	Weak transcription	Ovary	ovary
10	chr12:11287600-11312600	Weak transcription	NHDF-Ad	bronchial
11	chr12:11289000-11312000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:11291600-11321800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:11292400-11312600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:11294600-11313400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:11295600-11313400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr12:11295800-11318400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:11297400-11318400	Weak transcription	Thymus	Thymus
18	chr12:11297600-11315200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:11297800-11318400	Weak transcription	Aorta	Aorta
20	chr12:11297800-11318400	Weak transcription	Lung	lung
21	chr12:11297800-11321600	Weak transcription	Brain Angular Gyrus	brain
22	chr12:11298000-11313200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:11301000-11313000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:11301000-11318200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:11301600-11316600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr12:11301600-11318200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:11301600-11323200	Weak transcription	Colonic Mucosa	Colon
28	chr12:11302000-11311800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:11302000-11317800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr12:11302000-11321200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:11302200-11318400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:11302600-11323200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr12:11302800-11312000	Weak transcription	Right Ventricle	heart
34	chr12:11303800-11311600	Weak transcription	K562	blood
35	chr12:11303800-11313600	Weak transcription	Brain Substantia Nigra	brain
36	chr12:11303800-11318200	Weak transcription	Placenta	Placenta
37	chr12:11303800-11318400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr12:11303800-11323600	Weak transcription	Esophagus	oesophagus
39	chr12:11304000-11307800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr12:11304000-11308600	Weak transcription	Primary T cells from cord blood	blood
41	chr12:11304000-11309800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:11304000-11311600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:11304000-11311600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr12:11304000-11313000	Weak transcription	Fetal Stomach	stomach
45	chr12:11304000-11313400	Weak transcription	Fetal Thymus	thymus
46	chr12:11304000-11313600	Weak transcription	Left Ventricle	heart
47	chr12:11304000-11316600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr12:11304000-11318400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:11304000-11318400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:11304000-11321200	Weak transcription	Fetal Brain Male	brain

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