Variant report

Variant	rs2444256
Chromosome Location	chr2:152280365-152280366
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152144662..152146339-chr2:152277949..152280941,2	MCF-7	breast:
2	chr2:152268664..152271043-chr2:152277854..152280826,3	MCF-7	breast:
3	chr2:152265620..152268450-chr2:152279936..152282678,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000080345	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10173699	0.87[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs10175134	0.82[EUR][1000 genomes]
rs10197940	0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[ASN][1000 genomes]
rs10208356	0.84[ASN][1000 genomes]
rs10210990	0.84[ASN][1000 genomes]
rs1047957	0.83[CEU][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs1061305	0.91[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]
rs11693857	0.84[ASN][1000 genomes]
rs12618981	0.87[CEU][hapmap]
rs12994320	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13393021	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs13422366	0.83[ASN][1000 genomes]
rs13555	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs17806204	0.87[CEU][hapmap]
rs2288193	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs2290367	0.85[ASN][1000 genomes]
rs2290368	0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[ASN][1000 genomes]
rs2342911	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2432943	0.85[EUR][1000 genomes]
rs2432945	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2432946	0.91[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs2432953	0.83[EUR][1000 genomes]
rs2432956	0.84[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs2432957	0.96[LWK][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs2444264	0.91[LWK][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs4335940	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4467261	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4500942	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes]
rs4592848	0.87[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs4664045	0.83[ASN][1000 genomes]
rs4664423	0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[ASN][1000 genomes]
rs4664438	0.84[EUR][1000 genomes]
rs6718372	0.86[YRI][hapmap]
rs6719297	0.83[YRI][hapmap]
rs6724796	0.81[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs6731486	0.81[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs6735771	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72860233	0.86[EUR][1000 genomes]
rs7602715	0.85[JPT][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2444256	RIF1	Cis_1M	lymphoblastoid	RTeQTL
rs2444256	RIF1	cis	Skin Sun Exposed Lower leg	GTEx
rs2444256	RIF1	cis	Esophagus Muscularis	GTEx
rs2444256	RIF1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152267600-152287000	Weak transcription	Colonic Mucosa	Colon
2	chr2:152267600-152379400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:152267800-152340400	Weak transcription	Stomach Mucosa	stomach
4	chr2:152268000-152342800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr2:152268200-152282000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:152268200-152284200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:152268200-152303000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:152268200-152319400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:152268200-152320800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:152268200-152327800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:152268200-152328400	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr2:152268200-152328600	Strong transcription	Fetal Thymus	thymus
13	chr2:152268400-152280600	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr2:152268400-152282600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:152268400-152282600	Strong transcription	Osteobl	bone
16	chr2:152268400-152283200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr2:152268400-152298200	Strong transcription	Fetal Intestine Large	intestine
18	chr2:152268400-152327800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:152268600-152280400	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:152268600-152281800	Strong transcription	HUVEC	blood vessel
21	chr2:152268600-152283600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:152268600-152300200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:152268600-152319200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:152268600-152326800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:152268600-152327800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr2:152268600-152334400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:152268600-152342600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:152268800-152280600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:152268800-152283400	Strong transcription	Liver	Liver
30	chr2:152268800-152283800	Strong transcription	K562	blood
31	chr2:152268800-152299800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:152268800-152319600	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:152268800-152326800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:152268800-152327800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:152268800-152327800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:152269000-152281800	Strong transcription	Fetal Lung	lung
37	chr2:152269000-152284000	Strong transcription	Fetal Brain Female	brain
38	chr2:152269000-152284600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:152269200-152280800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:152269400-152282600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:152269400-152327200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:152270600-152283200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:152270600-152283800	Strong transcription	HepG2	liver
44	chr2:152272400-152280600	Strong transcription	Primary B cells from cord blood	blood
45	chr2:152272400-152282000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
46	chr2:152272400-152319200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:152272400-152327800	Strong transcription	Dnd41	blood
48	chr2:152272600-152283000	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr2:152272600-152283200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:152273400-152281800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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