Variant report

Variant	rs13387171
Chromosome Location	chr2:48543917-48543918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:48010207..48012260-chr2:48541505..48544232,2	K562	blood:
2	chr2:48542620..48544627-chr2:48553697..48556453,2	K562	blood:
3	chr2:48342619..48344591-chr2:48541998..48544325,2	K562	blood:
4	chr2:48492137..48494411-chr2:48542775..48545328,2	K562	blood:
5	chr2:48542112..48544368-chr2:48660786..48663458,2	MCF-7	breast:
6	chr2:48347369..48349943-chr2:48542903..48544986,2	MCF-7	breast:
7	chr2:48341598..48344591-chr2:48542825..48544946,2	K562	blood:
8	chr2:48535868..48537728-chr2:48543055..48544951,2	K562	blood:
9	chr2:48543010..48545052-chr2:48667149..48669274,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162869	Chromatin interaction
ENSG00000272663	Chromatin interaction
ENSG00000116062	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10153773	0.84[ASN][1000 genomes]
rs10174717	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10180295	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10186237	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10193072	0.96[ASN][1000 genomes]
rs10199431	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10208124	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11676168	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11682044	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11685861	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11690690	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12616792	0.85[ASN][1000 genomes]
rs12713008	0.85[ASN][1000 genomes]
rs12713009	0.85[ASN][1000 genomes]
rs13383364	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13385535	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13386751	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13388291	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13426834	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13432998	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471405	0.83[ASN][1000 genomes]
rs28806843	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28841370	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4290706	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4344965	0.81[AMR][1000 genomes]
rs4411759	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4547573	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4641990	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs56163539	0.81[EUR][1000 genomes]
rs56352447	0.96[ASN][1000 genomes]
rs57668696	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58660534	0.88[ASN][1000 genomes]
rs59264464	0.92[ASN][1000 genomes]
rs59412192	0.92[ASN][1000 genomes]
rs59761994	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60677957	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62136987	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137001	0.88[ASN][1000 genomes]
rs62137002	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62137003	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62137005	0.88[ASN][1000 genomes]
rs62137006	0.88[ASN][1000 genomes]
rs62137007	0.88[ASN][1000 genomes]
rs62137008	0.86[ASN][1000 genomes]
rs62137009	0.86[ASN][1000 genomes]
rs62137015	0.81[AMR][1000 genomes]
rs62138801	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545027	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545028	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6545029	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545030	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545034	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545035	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545036	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6712029	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6743757	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6757206	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72818493	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72820405	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72887649	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7340322	0.86[ASN][1000 genomes]
rs7562069	0.84[AMR][1000 genomes]
rs7562816	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7568960	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7574125	0.82[ASN][1000 genomes]
rs7579932	0.83[AMR][1000 genomes]
rs7600794	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7606104	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9309152	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48540600-48544000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr2:48540600-48544200	Active TSS	Brain Angular Gyrus	brain
3	chr2:48540600-48544600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr2:48540600-48547400	Active TSS	GM12878-XiMat	blood
5	chr2:48540800-48544000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:48540800-48544200	Active TSS	NHLF	lung
7	chr2:48541000-48544000	Active TSS	A549	lung
8	chr2:48541000-48544200	Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr2:48541000-48544200	Active TSS	Fetal Brain Female	brain
10	chr2:48541000-48544400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:48541200-48544000	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr2:48541200-48544200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr2:48541200-48544200	Active TSS	Muscle Satellite Cultured Cells	--
14	chr2:48541400-48544000	Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr2:48541400-48544200	Active TSS	HMEC	breast
16	chr2:48541400-48544400	Active TSS	K562	blood
17	chr2:48541400-48544400	Active TSS	NHEK	skin
18	chr2:48541800-48544200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:48542400-48544200	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr2:48542600-48544400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:48542600-48544600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:48542800-48544400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:48543000-48544400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr2:48543000-48544600	Flanking Active TSS	Dnd41	blood
25	chr2:48543200-48544000	Active TSS	HepG2	liver
26	chr2:48543200-48544200	Weak transcription	Small Intestine	intestine
27	chr2:48543200-48544200	Weak transcription	Spleen	Spleen
28	chr2:48543200-48553200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:48543400-48544200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:48543400-48544200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr2:48543400-48544200	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr2:48543400-48544200	Enhancers	Fetal Lung	lung
33	chr2:48543400-48544200	Weak transcription	Left Ventricle	heart
34	chr2:48543400-48544400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:48543400-48545600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:48543400-48546800	Weak transcription	Placenta	Placenta
37	chr2:48543400-48547800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:48543400-48551800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:48543400-48552000	Weak transcription	Stomach Mucosa	stomach
40	chr2:48543400-48553000	Weak transcription	Lung	lung
41	chr2:48543400-48553000	Weak transcription	Psoas Muscle	Psoas
42	chr2:48543400-48568600	Weak transcription	HSMM	muscle
43	chr2:48543600-48544000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:48543600-48544000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:48543600-48544000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr2:48543600-48544000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr2:48543600-48544000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr2:48543600-48544000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:48543600-48544000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:48543600-48544000	Weak transcription	Fetal Kidney	kidney

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