Variant report

Variant	rs12994320
Chromosome Location	chr2:152268805-152268806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152262551..152270893-chr2:152273971..152280003,13	K562	blood:
2	chr2:152260866..152263147-chr2:152268349..152271091,2	K562	blood:
3	chr2:152267122..152269845-chr2:152289424..152290955,2	K562	blood:
4	chr2:152268664..152271043-chr2:152277854..152280826,3	MCF-7	breast:
5	chr10:8100569..8103096-chr2:152267484..152269878,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000080345	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10173699	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10175134	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10206635	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1047957	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10490521	0.85[EUR][1000 genomes]
rs10497081	0.84[EUR][1000 genomes]
rs10497082	0.84[EUR][1000 genomes]
rs1061305	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11675385	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12616688	0.83[EUR][1000 genomes]
rs12616740	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12618981	0.86[EUR][1000 genomes]
rs13403719	0.86[ASN][1000 genomes]
rs13555	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17193268	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17806204	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2045025	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2288193	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2342911	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432942	0.87[ASN][1000 genomes]
rs2432943	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2432945	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2432946	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2432953	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2432954	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2432956	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2432957	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2444256	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2444264	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2444267	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4335940	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4467261	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4592848	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4664438	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5024580	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6718372	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6718653	0.83[ASN][1000 genomes]
rs6735771	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72860233	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7587301	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7608474	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv834418	chr2:152205803-152385516	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12994320	RIF1	Cis_1M	lymphoblastoid	RTeQTL
rs12994320	RIF1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152267400-152269000	Weak transcription	Lung	lung
2	chr2:152267400-152269000	Weak transcription	Pancreas	Pancrea
3	chr2:152267400-152276200	Weak transcription	Spleen	Spleen
4	chr2:152267600-152269000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:152267600-152269000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:152267600-152269000	Weak transcription	Ovary	ovary
7	chr2:152267600-152269000	Weak transcription	Right Ventricle	heart
8	chr2:152267600-152269800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:152267600-152270200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr2:152267600-152274800	Weak transcription	Thymus	Thymus
11	chr2:152267600-152276600	Weak transcription	Psoas Muscle	Psoas
12	chr2:152267600-152277400	Weak transcription	HSMMtube	muscle
13	chr2:152267600-152287000	Weak transcription	Colonic Mucosa	Colon
14	chr2:152267600-152379400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:152267800-152269200	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr2:152267800-152269200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:152267800-152269200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:152267800-152269600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:152267800-152269800	Weak transcription	Fetal Kidney	kidney
20	chr2:152267800-152275600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:152267800-152276000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:152267800-152276200	Weak transcription	Aorta	Aorta
23	chr2:152267800-152276200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:152267800-152340400	Weak transcription	Stomach Mucosa	stomach
25	chr2:152268000-152269000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:152268000-152269000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:152268000-152269000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr2:152268000-152269200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:152268000-152269200	Weak transcription	Brain Germinal Matrix	brain
30	chr2:152268000-152269200	Weak transcription	HMEC	breast
31	chr2:152268000-152269800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:152268000-152269800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:152268000-152270000	Weak transcription	Primary B cells from cord blood	blood
34	chr2:152268000-152270600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr2:152268000-152273400	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:152268000-152274000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:152268000-152342800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:152268200-152269200	Weak transcription	Brain Angular Gyrus	brain
39	chr2:152268200-152269200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:152268200-152269400	Transcr. at gene 5' and 3'	Dnd41	blood
41	chr2:152268200-152270600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr2:152268200-152270600	Genic enhancers	HepG2	liver
43	chr2:152268200-152272600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:152268200-152273400	Strong transcription	NHDF-Ad	bronchial
45	chr2:152268200-152276200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:152268200-152276200	Weak transcription	Fetal Brain Male	brain
47	chr2:152268200-152276800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:152268200-152278200	Strong transcription	HSMM	muscle
49	chr2:152268200-152278600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr2:152268200-152279200	Weak transcription	Small Intestine	intestine

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