Variant report

Variant	rs2432957
Chromosome Location	chr2:152287897-152287898
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152285997..152288359-chr2:152296614..152299198,2	K562	blood:
2	chr2:152283341..152286835-chr2:152286968..152289954,3	K562	blood:
3	chr2:152266206..152267961-chr2:152286037..152287966,2	MCF-7	breast:
4	chr2:152266232..152267827-chr2:152286440..152288453,2	K562	blood:
5	chr2:152285523..152288327-chr2:152289774..152291550,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000080345	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10167358	0.87[CHB][hapmap];0.88[CHD][hapmap]
rs10173699	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10175134	0.89[ASN][1000 genomes]
rs1047957	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10490521	0.82[ASN][1000 genomes]
rs10497081	0.85[ASN][1000 genomes]
rs10497082	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1061305	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11675385	0.87[ASN][1000 genomes]
rs11892439	0.87[CHB][hapmap]
rs12618981	0.87[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12994320	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13403719	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13425170	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs13555	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17270233	0.81[ASN][1000 genomes]
rs2045025	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2288193	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2288196	0.86[YRI][hapmap]
rs2342911	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2432942	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2432943	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2432945	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2432946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2432953	0.93[ASN][1000 genomes]
rs2432954	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2432956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2444256	0.96[LWK][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs2444264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2444267	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3771901	0.86[CHD][hapmap]
rs4335940	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4461258	0.81[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap]
rs4467261	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4592848	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4664438	0.91[ASN][1000 genomes]
rs4664490	0.80[CHB][hapmap]
rs4664491	0.87[CHB][hapmap]
rs5024580	0.82[ASN][1000 genomes]
rs6718372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6718653	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6721666	0.86[YRI][hapmap]
rs6730454	0.86[YRI][hapmap]
rs6735771	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72860233	0.97[ASN][1000 genomes]
rs7587301	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7608474	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9287979	0.80[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2432957	RIF1	Cis_1M	lymphoblastoid	RTeQTL
rs2432957	RIF1	cis	parietal	SCAN

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	chr2:152274600-152290400	Strong transcription	Fetal Muscle Leg	muscle
27	chr2:152274800-152289000	Strong transcription	Fetal Stomach	stomach
28	chr2:152275800-152310000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:152277000-152294200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr2:152277000-152301400	Weak transcription	Fetal Heart	heart
31	chr2:152278200-152290000	Weak transcription	Esophagus	oesophagus
32	chr2:152278200-152293600	Weak transcription	Brain Angular Gyrus	brain
33	chr2:152278200-152294200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:152278400-152293400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:152278600-152290000	Weak transcription	Aorta	Aorta
36	chr2:152278600-152310200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:152280000-152288600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:152280000-152291600	Weak transcription	Fetal Kidney	kidney
39	chr2:152280000-152294000	Weak transcription	Gastric	stomach
40	chr2:152280200-152292800	Weak transcription	Brain Substantia Nigra	brain
41	chr2:152280600-152288200	Weak transcription	Primary B cells from cord blood	blood
42	chr2:152280600-152288600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:152280600-152289000	Strong transcription	Fetal Intestine Small	intestine
44	chr2:152281000-152292000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:152281600-152292600	Weak transcription	Pancreas	Pancrea
46	chr2:152282000-152291800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:152282600-152290000	Strong transcription	Fetal Lung	lung
48	chr2:152282600-152313800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:152282800-152315800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:152283400-152292400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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