Variant report

Variant	rs10173699
Chromosome Location	chr2:152281561-152281562
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152265620..152268450-chr2:152279936..152282678,3	MCF-7	breast:
2	chr2:152280542..152282087-chr2:152301597..152303265,2	K562	blood:

Variant related genes	Relation type
ENSG00000080345	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10167358	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap]
rs10175134	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10206635	0.83[EUR][1000 genomes]
rs1047957	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10490521	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10497081	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10497082	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1061305	0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11675385	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11892439	0.87[CHB][hapmap]
rs12616688	0.80[EUR][1000 genomes]
rs12616740	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12618981	0.91[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12994320	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13393021	0.91[CEU][hapmap]
rs13403719	0.91[ASN][1000 genomes]
rs13425170	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs13555	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17193268	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17270233	0.81[ASN][1000 genomes]
rs17806204	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2045025	0.91[ASN][1000 genomes]
rs2288193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2342911	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2432942	0.88[ASN][1000 genomes]
rs2432943	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2432945	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432946	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2432953	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2432954	0.90[ASN][1000 genomes]
rs2432956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2432957	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2444256	0.87[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs2444264	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2444267	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3771901	0.82[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs4335940	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4461258	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs4467261	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4500942	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs4592848	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4664438	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4664490	0.80[CHB][hapmap];0.88[GIH][hapmap]
rs4664491	0.87[CHB][hapmap]
rs5024580	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6718372	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6718653	0.89[ASN][1000 genomes]
rs6724796	0.91[CEU][hapmap];0.92[TSI][hapmap]
rs6731486	0.91[CEU][hapmap];0.92[TSI][hapmap]
rs6735771	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72860233	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7587301	0.90[ASN][1000 genomes]
rs7608474	0.88[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10173699	RIF1	cis	Skin Sun Exposed Lower leg	GTEx
rs10173699	RIF1	cis	parietal	SCAN
rs10173699	RIF1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152267600-152287000	Weak transcription	Colonic Mucosa	Colon
2	chr2:152267600-152379400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:152267800-152340400	Weak transcription	Stomach Mucosa	stomach
4	chr2:152268000-152342800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:152268200-152282000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:152268200-152284200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:152268200-152303000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:152268200-152319400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:152268200-152320800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:152268200-152327800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:152268200-152328400	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr2:152268200-152328600	Strong transcription	Fetal Thymus	thymus
13	chr2:152268400-152282600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:152268400-152282600	Strong transcription	Osteobl	bone
15	chr2:152268400-152283200	Strong transcription	Duodenum Mucosa	Duodenum
16	chr2:152268400-152298200	Strong transcription	Fetal Intestine Large	intestine
17	chr2:152268400-152327800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr2:152268600-152281800	Strong transcription	HUVEC	blood vessel
19	chr2:152268600-152283600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:152268600-152300200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr2:152268600-152319200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:152268600-152326800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:152268600-152327800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:152268600-152334400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:152268600-152342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:152268800-152283400	Strong transcription	Liver	Liver
27	chr2:152268800-152283800	Strong transcription	K562	blood
28	chr2:152268800-152299800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:152268800-152319600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:152268800-152326800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:152268800-152327800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:152268800-152327800	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr2:152269000-152281800	Strong transcription	Fetal Lung	lung
34	chr2:152269000-152284000	Strong transcription	Fetal Brain Female	brain
35	chr2:152269000-152284600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:152269400-152282600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:152269400-152327200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:152270600-152283200	Strong transcription	Fetal Muscle Trunk	muscle
39	chr2:152270600-152283800	Strong transcription	HepG2	liver
40	chr2:152272400-152282000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:152272400-152319200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:152272400-152327800	Strong transcription	Dnd41	blood
43	chr2:152272600-152283000	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr2:152272600-152283200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:152273400-152281800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:152274600-152290400	Strong transcription	Fetal Muscle Leg	muscle
47	chr2:152274800-152289000	Strong transcription	Fetal Stomach	stomach
48	chr2:152275600-152282600	Strong transcription	NHDF-Ad	bronchial
49	chr2:152275800-152310000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:152276000-152281800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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