Variant report

Variant	rs2432940
Chromosome Location	chr2:152300949-152300950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152265589..152267919-chr2:152300372..152303001,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000080345	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10432479	0.80[ASN][1000 genomes]
rs1065177	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13002073	0.86[AFR][1000 genomes]
rs13391309	0.80[ASN][1000 genomes]
rs2123465	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2288195	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2288198	0.80[ASN][1000 genomes]
rs2432936	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2432938	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2432941	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2432944	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2432951	0.86[AFR][1000 genomes]
rs2444257	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2444259	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2444260	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2444262	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2444263	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2444266	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2444270	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2444272	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2444274	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3771900	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3815851	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4315520	0.82[AFR][1000 genomes]
rs4474880	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4664455	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4994327	0.84[ASN][1000 genomes]
rs7558940	0.80[ASN][1000 genomes]
rs7585717	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
rs2432940	RIF1	cis	Artery Tibial	GTEx
rs2432940	RIF1	cis	Nerve Tibial	GTEx
rs2432940	RIF1	Cis_1M	lymphoblastoid	RTeQTL
rs2432940	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	chr2:152268400-152327800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:152268600-152319200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:152268600-152326800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:152268600-152327800	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:152268600-152334400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:152268600-152342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:152268800-152319600	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:152268800-152326800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:152268800-152327800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:152268800-152327800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr2:152269400-152327200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:152272400-152319200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:152272400-152327800	Strong transcription	Dnd41	blood
23	chr2:152275800-152310000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:152277000-152301400	Weak transcription	Fetal Heart	heart
25	chr2:152278600-152310200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:152282600-152313800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:152282800-152315800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:152283800-152334000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr2:152284200-152327000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:152284600-152327800	Strong transcription	HepG2	liver
31	chr2:152285000-152303400	Strong transcription	Osteobl	bone
32	chr2:152285000-152314200	Strong transcription	HMEC	breast
33	chr2:152285000-152327800	Strong transcription	Placenta	Placenta
34	chr2:152285200-152306200	Strong transcription	Liver	Liver
35	chr2:152285200-152306200	Strong transcription	HSMM	muscle
36	chr2:152285200-152315400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:152285200-152327600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:152285200-152327800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:152285200-152331200	Strong transcription	Adipose Nuclei	Adipose
40	chr2:152285600-152308400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:152288800-152304200	Weak transcription	Colonic Mucosa	Colon
42	chr2:152288800-152309200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:152289400-152301200	Weak transcription	Small Intestine	intestine
44	chr2:152290600-152323400	Weak transcription	Aorta	Aorta
45	chr2:152291400-152314600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr2:152291800-152312400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:152291800-152321000	Strong transcription	Duodenum Mucosa	Duodenum
48	chr2:152292200-152307400	Strong transcription	Fetal Intestine Small	intestine
49	chr2:152293000-152313000	Strong transcription	A549	lung
50	chr2:152293600-152312000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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