Variant report

Variant	rs2444257
Chromosome Location	chr2:152322095-152322096
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10182296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[ASN][1000 genomes]
rs10187997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs10432479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs1065177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13002073	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13391309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2123465	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2288195	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2288198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2288201	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2288210	0.83[YRI][hapmap]
rs2432936	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2432938	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2432940	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2432941	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2432944	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2432951	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2444259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2444260	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2444262	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2444263	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2444266	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2444270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2444272	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2444274	0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3771900	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3815851	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3815852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4233649	0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4233650	0.83[ASN][1000 genomes]
rs4233651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4315520	0.86[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs4474880	0.97[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4664055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[ASN][1000 genomes]
rs4664065	0.84[CHB][hapmap]
rs4664455	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4664493	0.82[CHB][hapmap]
rs4994327	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6433481	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6433482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[ASN][1000 genomes]
rs6707824	0.84[CHB][hapmap]
rs6715917	0.89[ASN][1000 genomes]
rs6719297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs6725513	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.80[ASN][1000 genomes]
rs6735678	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap]
rs7419956	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7422136	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs7558940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7563568	0.80[ASN][1000 genomes]
rs7566225	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7575451	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7585717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7597735	0.93[JPT][hapmap];0.86[YRI][hapmap]
rs9287981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs9287982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[ASN][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	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
2	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
3	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
4	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
5	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
6	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
7	nsv933869	chr2:152308156-152391576	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv934136	chr2:152308156-152664443	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv437298	chr2:152320118-152356361	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv3693428	chr2:152320932-152434896	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv438374	chr2:152322095-152331418	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2444257	RIF1	Cis_1M	lymphoblastoid	RTeQTL
rs2444257	RIF1	cis	Esophagus Muscularis	GTEx
rs2444257	RIF1	cis	Skin Sun Exposed Lower leg	GTEx
rs2444257	RIF1	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152267600-152379400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:152267800-152340400	Weak transcription	Stomach Mucosa	stomach
3	chr2:152268000-152342800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:152268200-152327800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:152268200-152328400	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr2:152268200-152328600	Strong transcription	Fetal Thymus	thymus
7	chr2:152268400-152327800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:152268600-152326800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:152268600-152327800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr2:152268600-152334400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:152268600-152342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:152268800-152326800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:152268800-152327800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:152268800-152327800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:152269400-152327200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:152272400-152327800	Strong transcription	Dnd41	blood
17	chr2:152283800-152334000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr2:152284200-152327000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:152284600-152327800	Strong transcription	HepG2	liver
20	chr2:152285000-152327800	Strong transcription	Placenta	Placenta
21	chr2:152285200-152327600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:152285200-152327800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:152285200-152331200	Strong transcription	Adipose Nuclei	Adipose
24	chr2:152290600-152323400	Weak transcription	Aorta	Aorta
25	chr2:152294600-152327800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:152294800-152327800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:152295800-152348400	Weak transcription	Right Ventricle	heart
28	chr2:152298600-152327600	Strong transcription	HUVEC	blood vessel
29	chr2:152300000-152333400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:152300200-152327800	Strong transcription	K562	blood
31	chr2:152301600-152324400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:152301800-152343800	Weak transcription	Gastric	stomach
33	chr2:152303200-152325000	Weak transcription	Small Intestine	intestine
34	chr2:152303400-152326400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:152304800-152322800	Strong transcription	Osteobl	bone
36	chr2:152304800-152354000	Weak transcription	Spleen	Spleen
37	chr2:152306200-152322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:152306400-152324800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:152306800-152328400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:152307000-152328000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr2:152307600-152327600	Strong transcription	Primary B cells from cord blood	blood
42	chr2:152307600-152327800	Strong transcription	HSMM	muscle
43	chr2:152307600-152328000	Strong transcription	Liver	Liver
44	chr2:152309000-152327800	Strong transcription	Fetal Intestine Large	intestine
45	chr2:152311800-152323600	Strong transcription	Fetal Kidney	kidney
46	chr2:152312000-152327600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr2:152314000-152324200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:152314000-152344000	Weak transcription	Esophagus	oesophagus
49	chr2:152314000-152349400	Weak transcription	Pancreas	Pancrea
50	chr2:152314400-152322600	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links