Variant report

Variant	rs2444263
Chromosome Location	chr2:152311570-152311571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152310372..152313299-chr2:152315100..152317140,2	K562	blood:
2	chr2:152302369..152305079-chr2:152310226..152311747,2	K562	blood:
3	chr2:152306334..152309706-chr2:152310783..152314645,4	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10182296	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs10187997	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs10432479	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[TSI][hapmap];0.90[YRI][hapmap];0.89[ASN][1000 genomes]
rs1065177	0.88[ASW][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10930688	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12996964	0.92[CHD][hapmap]
rs13002073	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13391309	0.88[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2123465	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288198	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[TSI][hapmap];0.89[ASN][1000 genomes]
rs2288201	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2288210	0.85[YRI][hapmap]
rs2432936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2432938	0.92[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2432940	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2432941	0.88[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2432944	0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2432951	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2444257	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2444259	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2444260	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2444262	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2444266	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2444270	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2444272	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2444274	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771900	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3815851	0.88[ASW][hapmap];0.83[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3815852	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[ASN][1000 genomes]
rs4233649	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4233650	0.84[ASN][1000 genomes]
rs4233651	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4315520	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4474880	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664055	0.88[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs4664455	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4664475	0.81[TSI][hapmap]
rs4664486	0.81[TSI][hapmap]
rs4664493	0.88[CHD][hapmap]
rs4994327	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6433481	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6433482	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs6707824	0.92[CHB][hapmap]
rs6715917	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6719297	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs6725513	0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs6735678	0.88[ASW][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.80[ASN][1000 genomes]
rs7419413	0.82[YRI][hapmap]
rs7419956	0.88[ASW][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7422136	0.92[CHD][hapmap];0.82[YRI][hapmap]
rs7424331	0.85[YRI][hapmap]
rs7558940	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7563568	0.81[ASN][1000 genomes]
rs7566225	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7575451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7585717	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.86[TSI][hapmap];0.89[ASN][1000 genomes]
rs7597735	0.93[JPT][hapmap];0.86[YRI][hapmap]
rs9287981	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs9287982	0.88[ASW][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs9287983	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv3693427	chr2:152303171-152320118	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	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
9	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2444263	RIF1	cis	parietal	SCAN
rs2444263	RIF1	cis	Artery Tibial	GTEx
rs2444263	RIF1	cis	Skin Sun Exposed Lower leg	GTEx
rs2444263	RND3	cis	parietal	SCAN
rs2444263	RIF1	Cis_1M	lymphoblastoid	RTeQTL
rs2444263	RIF1	cis	Esophagus Muscularis	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	chr2:152268200-152319400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr2:152268200-152320800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:152268200-152327800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:152268200-152328400	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr2:152268200-152328600	Strong transcription	Fetal Thymus	thymus
9	chr2:152268400-152327800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr2:152268600-152319200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:152268600-152326800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:152268600-152327800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr2:152268600-152334400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:152268600-152342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:152268800-152319600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:152268800-152326800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:152268800-152327800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:152268800-152327800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:152269400-152327200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:152272400-152319200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:152272400-152327800	Strong transcription	Dnd41	blood
22	chr2:152282600-152313800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:152282800-152315800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:152283800-152334000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr2:152284200-152327000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:152284600-152327800	Strong transcription	HepG2	liver
27	chr2:152285000-152314200	Strong transcription	HMEC	breast
28	chr2:152285000-152327800	Strong transcription	Placenta	Placenta
29	chr2:152285200-152315400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:152285200-152327600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:152285200-152327800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:152285200-152331200	Strong transcription	Adipose Nuclei	Adipose
33	chr2:152290600-152323400	Weak transcription	Aorta	Aorta
34	chr2:152291400-152314600	Strong transcription	Primary B cells from peripheral blood	blood
35	chr2:152291800-152312400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:152291800-152321000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr2:152293000-152313000	Strong transcription	A549	lung
38	chr2:152293600-152312000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:152294400-152321400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:152294600-152327800	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:152294800-152327800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:152295600-152313400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:152295800-152348400	Weak transcription	Right Ventricle	heart
44	chr2:152298600-152327600	Strong transcription	HUVEC	blood vessel
45	chr2:152298800-152312800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:152300000-152313600	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:152300000-152333400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:152300200-152327800	Strong transcription	K562	blood
49	chr2:152301000-152319200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:152301400-152312400	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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