Variant report

Variant	rs12828263
Chromosome Location	chr12:75903206-75903207
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	chr12:75901516..75903864-chr12:75903925..75905942,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111615	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs4472973	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription 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	12 gene(s)	inside rSNPs	diseases
6	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12828263	GLIPR1L2	cis	parietal	SCAN
rs12828263	GLIPR1L2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75875600-75903400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:75875800-75903600	Weak transcription	Fetal Intestine Small	intestine
3	chr12:75876200-75903400	Weak transcription	Fetal Stomach	stomach
4	chr12:75880600-75903800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:75883800-75904800	Weak transcription	Esophagus	oesophagus
6	chr12:75888800-75903800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:75888800-75904200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:75891400-75903800	Weak transcription	Fetal Brain Male	brain
9	chr12:75892800-75904400	Weak transcription	Gastric	stomach
10	chr12:75893800-75903600	Weak transcription	Stomach Mucosa	stomach
11	chr12:75895400-75903800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:75895400-75903800	Weak transcription	Brain Substantia Nigra	brain
13	chr12:75895400-75904000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:75895400-75904200	Weak transcription	Right Ventricle	heart
15	chr12:75895400-75904400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:75895400-75904600	Weak transcription	Lung	lung
17	chr12:75895600-75904000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:75895800-75904800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:75896000-75903600	Weak transcription	Brain Angular Gyrus	brain
20	chr12:75896200-75904000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr12:75896400-75903800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:75896400-75904000	Weak transcription	Fetal Heart	heart
23	chr12:75897000-75903400	Weak transcription	Fetal Brain Female	brain
24	chr12:75897000-75903600	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:75897000-75904000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:75897000-75904600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:75897200-75903800	Weak transcription	Brain Anterior Caudate	brain
28	chr12:75897400-75903400	Weak transcription	Psoas Muscle	Psoas
29	chr12:75897400-75903800	Weak transcription	Brain Germinal Matrix	brain
30	chr12:75897400-75904000	Weak transcription	Aorta	Aorta
31	chr12:75897600-75903600	Weak transcription	Thymus	Thymus
32	chr12:75897600-75904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr12:75897600-75904800	Weak transcription	Spleen	Spleen
34	chr12:75897800-75904000	Weak transcription	Colonic Mucosa	Colon
35	chr12:75897800-75904600	Weak transcription	Left Ventricle	heart
36	chr12:75897800-75904800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:75898000-75903400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:75898000-75903800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:75898800-75903400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:75899600-75903800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:75899600-75903800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr12:75900000-75903400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:75900000-75904400	Weak transcription	Fetal Muscle Leg	muscle
44	chr12:75900200-75903800	Weak transcription	HSMMtube	muscle
45	chr12:75900400-75904600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr12:75900600-75903400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr12:75900600-75903400	Weak transcription	Fetal Intestine Large	intestine
48	chr12:75900800-75903400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:75900800-75903600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:75900800-75903800	Weak transcription	Fetal Lung	lung

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