Variant report

Variant	rs12313999
Chromosome Location	chr12:118477182-118477183
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118476730..118480005-chr12:118496581..118498795,3	K562	blood:
2	chr12:118475337..118478280-chr12:118499969..118502242,2	MCF-7	breast:
3	chr12:118455151..118457113-chr12:118475615..118477971,2	MCF-7	breast:
4	chr12:118472870..118474634-chr12:118475907..118478389,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176871	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11068779	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068782	0.94[YRI][hapmap]
rs11068788	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309202	0.85[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12578639	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579444	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580039	0.89[CHB][hapmap];0.89[MEX][hapmap]
rs12582265	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55973710	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745792	0.82[AMR][1000 genomes]
rs5745807	0.82[CEU][hapmap];0.89[CHB][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes]
rs5745808	0.80[AMR][1000 genomes]
rs5745820	0.82[AMR][1000 genomes]
rs5745876	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.92[ASN][1000 genomes]
rs57493385	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58116528	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58436126	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58639682	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60777883	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61094951	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7485548	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488835	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560388	chr12:118391600-118482352	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv1795965	chr12:118463329-118504859	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12313999	RPLP0	cis	cerebellum	SCAN
rs12313999	CCDC42B	cis	cerebellum	SCAN
rs12313999	SLC24A6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118455200-118497400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:118455600-118490200	Strong transcription	Fetal Muscle Trunk	muscle
3	chr12:118455800-118485000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:118455800-118490000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:118456000-118478000	Weak transcription	Fetal Heart	heart
6	chr12:118456000-118482800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:118456000-118484600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:118456000-118490200	Strong transcription	Fetal Stomach	stomach
9	chr12:118456200-118484000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:118456200-118484200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:118456200-118484600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:118456200-118490000	Strong transcription	Fetal Muscle Leg	muscle
13	chr12:118456200-118490200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:118456200-118490400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:118456400-118489800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:118456400-118491000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:118456600-118477400	Strong transcription	Fetal Thymus	thymus
18	chr12:118456600-118482800	Strong transcription	Primary T cells from cord blood	blood
19	chr12:118456600-118489800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr12:118456800-118482000	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr12:118456800-118484000	Strong transcription	Stomach Smooth Muscle	stomach
22	chr12:118456800-118489400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:118456800-118489800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:118457000-118482600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr12:118457000-118482800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:118457000-118482800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:118457000-118484600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:118457000-118488200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr12:118457000-118489600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr12:118457200-118483000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:118457200-118491400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:118457600-118482400	Strong transcription	Thymus	Thymus
33	chr12:118458200-118481600	Strong transcription	Dnd41	blood
34	chr12:118459800-118491000	Strong transcription	Fetal Brain Female	brain
35	chr12:118462200-118488400	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:118462400-118482800	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr12:118462600-118482200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr12:118462600-118489000	Strong transcription	Fetal Intestine Large	intestine
39	chr12:118462800-118483000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr12:118462800-118484000	Strong transcription	Fetal Lung	lung
41	chr12:118462800-118484000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:118462800-118484600	Strong transcription	Brain Germinal Matrix	brain
43	chr12:118465000-118481000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:118466600-118482800	Strong transcription	Ovary	ovary
45	chr12:118467200-118489400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:118467400-118481000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:118467600-118482600	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:118467600-118482800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr12:118467800-118481200	Strong transcription	HSMM	muscle
50	chr12:118467800-118481600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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