Variant report

Variant	rs2444272
Chromosome Location	chr2:152293620-152293621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152293439..152294985-chr2:152313987..152316926,2	K562	blood:
2	chr2:152117421..152121321-chr2:152293142..152295982,3	MCF-7	breast:
3	chr2:152291790..152293489-chr2:152293585..152295712,2	MCF-7	breast:
4	chr2:152288811..152290413-chr2:152292580..152295244,2	K562	blood:
5	chr2:152288510..152290413-chr2:152292580..152296042,3	K562	blood:

Variant related genes	Relation type
ENSG00000184898	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10182296	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[ASN][1000 genomes]
rs10187997	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs10432479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[ASN][1000 genomes]
rs1065177	0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10930688	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13002073	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13391309	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2123465	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288195	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2288201	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2288210	0.85[YRI][hapmap]
rs2432936	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2432938	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2432940	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2432941	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2432944	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2432951	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2444257	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2444259	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2444260	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2444262	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2444263	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]
rs2444266	0.97[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2444270	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2444274	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771900	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3815851	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3815852	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4233649	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4233650	0.85[ASN][1000 genomes]
rs4233651	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4315520	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4474880	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4664055	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[ASN][1000 genomes]
rs4664065	0.81[CHB][hapmap]
rs4664455	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4994327	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6433481	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6433482	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs6707824	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6715917	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6719297	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[ASN][1000 genomes]
rs6725513	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[ASN][1000 genomes]
rs6735678	0.89[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs7419413	0.86[YRI][hapmap]
rs7419956	0.88[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7422136	0.92[YRI][hapmap]
rs7424331	0.85[YRI][hapmap]
rs7558940	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7563568	0.82[ASN][1000 genomes]
rs7566225	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7568873	0.85[YRI][hapmap]
rs7575451	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7585717	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7597735	0.92[JPT][hapmap];0.89[YRI][hapmap]
rs9287981	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs9287982	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2444272	RIF1	Cis_1M	lymphoblastoid	RTeQTL
rs2444272	RIF1	cis	Artery Tibial	GTEx
rs2444272	RIF1	cis	Esophagus Muscularis	GTEx
rs2444272	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	chr2:152267600-152379400	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	chr2:152268200-152303000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:152268200-152319400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:152268200-152320800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:152268200-152327800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:152268200-152328400	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr2:152268200-152328600	Strong transcription	Fetal Thymus	thymus
10	chr2:152268400-152298200	Strong transcription	Fetal Intestine Large	intestine
11	chr2:152268400-152327800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:152268600-152300200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:152268600-152319200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:152268600-152326800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:152268600-152327800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr2:152268600-152334400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:152268600-152342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:152268800-152299800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:152268800-152319600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:152268800-152326800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:152268800-152327800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:152268800-152327800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:152269400-152327200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:152272400-152319200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:152272400-152327800	Strong transcription	Dnd41	blood
26	chr2:152275800-152310000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:152277000-152294200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr2:152277000-152301400	Weak transcription	Fetal Heart	heart
29	chr2:152278200-152294200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:152278600-152310200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:152280000-152294000	Weak transcription	Gastric	stomach
32	chr2:152282600-152313800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:152282800-152315800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:152283800-152294400	Weak transcription	NHEK	skin
35	chr2:152283800-152334000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr2:152284000-152296400	Strong transcription	HUVEC	blood vessel
37	chr2:152284200-152327000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:152284600-152327800	Strong transcription	HepG2	liver
39	chr2:152284800-152293800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr2:152285000-152294000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:152285000-152294200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:152285000-152299000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:152285000-152303400	Strong transcription	Osteobl	bone
44	chr2:152285000-152314200	Strong transcription	HMEC	breast
45	chr2:152285000-152327800	Strong transcription	Placenta	Placenta
46	chr2:152285200-152295400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr2:152285200-152297200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:152285200-152298000	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:152285200-152298000	Strong transcription	GM12878-XiMat	blood
50	chr2:152285200-152306200	Strong transcription	Liver	Liver

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