Variant report

Variant	rs4315520
Chromosome Location	chr2:152271907-152271908
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:152271832-152272075	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:152270230..152272767-chr2:152284847..152286605,2	K562	blood:
2	chr2:152265525..152267360-chr2:152270009..152272333,3	MCF-7	breast:
3	chr2:152265555..152269116-chr2:152269782..152271930,3	MCF-7	breast:

Variant related genes	Relation type
RIF1	TF binding region
ENSG00000080345	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10182296	0.86[JPT][hapmap];0.85[YRI][hapmap]
rs10187997	0.92[JPT][hapmap];0.92[YRI][hapmap]
rs10432479	0.85[CHD][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap]
rs1065177	0.88[ASW][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.87[MKK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs10930688	0.86[JPT][hapmap]
rs12996964	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs13002073	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13391309	0.87[ASW][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap]
rs2123465	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2288195	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2288198	0.85[CHD][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];0.88[TSI][hapmap]
rs2288201	0.86[JPT][hapmap];0.82[YRI][hapmap]
rs2288210	0.92[JPT][hapmap];0.85[YRI][hapmap]
rs2432936	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2432938	0.82[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap]
rs2432940	0.82[AFR][1000 genomes]
rs2432941	0.88[ASW][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs2432944	0.89[AFR][1000 genomes]
rs2432951	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2444257	0.86[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2444259	0.86[JPT][hapmap]
rs2444260	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2444262	0.87[AFR][1000 genomes]
rs2444263	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]
rs2444266	0.87[AFR][1000 genomes]
rs2444270	0.86[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2444272	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]
rs2444274	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3771900	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3815851	0.88[ASW][hapmap];0.81[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs3815852	0.85[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap]
rs4233651	0.92[JPT][hapmap]
rs4474880	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4664055	0.88[ASW][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs4664455	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4664475	0.80[TSI][hapmap]
rs4994327	0.82[CEU][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs6433481	0.86[JPT][hapmap]
rs6433482	0.86[JPT][hapmap];0.92[YRI][hapmap]
rs6707824	0.81[CEU][hapmap];0.92[JPT][hapmap]
rs6715917	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6719297	0.85[CHD][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap]
rs6725513	0.92[YRI][hapmap]
rs6735678	0.88[ASW][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap]
rs7419413	0.92[JPT][hapmap];0.82[YRI][hapmap]
rs7419956	0.88[ASW][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap]
rs7422136	0.82[CHD][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap]
rs7424331	0.85[YRI][hapmap]
rs7558940	0.86[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs7566225	0.81[AFR][1000 genomes]
rs7568873	0.92[JPT][hapmap]
rs7575451	0.86[JPT][hapmap];0.92[YRI][hapmap]
rs7585717	0.85[CHD][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];0.83[TSI][hapmap]
rs7597735	0.81[JPT][hapmap];0.82[YRI][hapmap]
rs9287981	0.86[JPT][hapmap];0.92[YRI][hapmap]
rs9287982	0.88[ASW][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4315520	RIF1	cis	parietal	SCAN
rs4315520	RIF1	cis	Esophagus Muscularis	GTEx
rs4315520	RIF1	cis	Artery Tibial	GTEx
rs4315520	RIF1	cis	Skin Sun Exposed Lower leg	GTEx
rs4315520	RND3	cis	parietal	SCAN
rs4315520	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	chr2:152267400-152276200	Weak transcription	Spleen	Spleen
2	chr2:152267600-152274800	Weak transcription	Thymus	Thymus
3	chr2:152267600-152276600	Weak transcription	Psoas Muscle	Psoas
4	chr2:152267600-152277400	Weak transcription	HSMMtube	muscle
5	chr2:152267600-152287000	Weak transcription	Colonic Mucosa	Colon
6	chr2:152267600-152379400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:152267800-152275600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:152267800-152276000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:152267800-152276200	Weak transcription	Aorta	Aorta
10	chr2:152267800-152276200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:152267800-152340400	Weak transcription	Stomach Mucosa	stomach
12	chr2:152268000-152273400	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:152268000-152274000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:152268000-152342800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:152268200-152272600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:152268200-152273400	Strong transcription	NHDF-Ad	bronchial
17	chr2:152268200-152276200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:152268200-152276200	Weak transcription	Fetal Brain Male	brain
19	chr2:152268200-152276800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:152268200-152278200	Strong transcription	HSMM	muscle
21	chr2:152268200-152278600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr2:152268200-152279200	Weak transcription	Small Intestine	intestine
23	chr2:152268200-152279800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr2:152268200-152282000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:152268200-152284200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:152268200-152303000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:152268200-152319400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:152268200-152320800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:152268200-152327800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:152268200-152328400	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr2:152268200-152328600	Strong transcription	Fetal Thymus	thymus
32	chr2:152268400-152274200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:152268400-152274600	Strong transcription	Placenta	Placenta
34	chr2:152268400-152274600	Strong transcription	NHLF	lung
35	chr2:152268400-152280600	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr2:152268400-152282600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:152268400-152282600	Strong transcription	Osteobl	bone
38	chr2:152268400-152283200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr2:152268400-152298200	Strong transcription	Fetal Intestine Large	intestine
40	chr2:152268400-152327800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr2:152268600-152272400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:152268600-152272400	Strong transcription	Fetal Stomach	stomach
43	chr2:152268600-152272600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:152268600-152272600	Strong transcription	Brain Anterior Caudate	brain
45	chr2:152268600-152272600	Strong transcription	Fetal Muscle Leg	muscle
46	chr2:152268600-152272800	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:152268600-152273000	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:152268600-152276200	Weak transcription	Fetal Heart	heart
49	chr2:152268600-152276800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr2:152268600-152278600	Strong transcription	Muscle Satellite Cultured Cells	--

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