Variant report

Variant	rs1489
Chromosome Location	chr5:74907334-74907335
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	chr5:74806025..74808781-chr5:74906137..74908952,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POC5-4	chr5:74907076-74907508	NONHSAT102214

Variant related genes	Relation type
ENSG00000122008	Chromatin interaction
ENSG00000113163	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11948350	0.94[EUR][1000 genomes]
rs11948442	0.94[EUR][1000 genomes]
rs11952534	0.94[EUR][1000 genomes]
rs11953173	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11953883	0.94[EUR][1000 genomes]
rs11955568	0.94[EUR][1000 genomes]
rs11955819	0.94[EUR][1000 genomes]
rs11956111	0.94[EUR][1000 genomes]
rs11956112	0.94[EUR][1000 genomes]
rs11956755	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11960741	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11960747	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11960771	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1422441	0.94[EUR][1000 genomes]
rs16872590	1.00[EUR][1000 genomes]
rs16872661	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16872677	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16872683	0.94[EUR][1000 genomes]
rs16872693	0.94[EUR][1000 genomes]
rs1991450	0.94[EUR][1000 genomes]
rs2112348	0.94[EUR][1000 genomes]
rs2112349	0.89[EUR][1000 genomes]
rs2112350	0.94[EUR][1000 genomes]
rs4640773	0.88[EUR][1000 genomes]
rs56832737	0.94[EUR][1000 genomes]
rs57414757	0.94[EUR][1000 genomes]
rs5744617	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5744720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57531042	0.94[EUR][1000 genomes]
rs57670471	0.94[EUR][1000 genomes]
rs58216239	0.94[EUR][1000 genomes]
rs59427628	0.94[EUR][1000 genomes]
rs60385047	0.94[EUR][1000 genomes]
rs60609097	0.94[EUR][1000 genomes]
rs61516153	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6865606	0.94[EUR][1000 genomes]
rs6866607	0.82[EUR][1000 genomes]
rs6870090	0.94[EUR][1000 genomes]
rs6882452	0.94[EUR][1000 genomes]
rs6894068	0.94[EUR][1000 genomes]
rs6895148	0.94[EUR][1000 genomes]
rs6898308	0.82[EUR][1000 genomes]
rs73120804	0.94[EUR][1000 genomes]
rs73120805	0.94[EUR][1000 genomes]
rs73120807	0.94[EUR][1000 genomes]
rs73120811	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73120822	0.94[EUR][1000 genomes]
rs73120824	0.94[EUR][1000 genomes]
rs73120848	1.00[EUR][1000 genomes]
rs73120849	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73120850	1.00[EUR][1000 genomes]
rs73122744	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73122755	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73122770	0.94[EUR][1000 genomes]
rs73122771	0.94[EUR][1000 genomes]
rs73122772	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73124734	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73124747	0.94[EUR][1000 genomes]
rs73124750	0.94[EUR][1000 genomes]
rs7722940	0.82[EUR][1000 genomes]
rs7724771	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882193	chr5:74656175-74917862	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv882196	chr5:74678937-74917862	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv882202	chr5:74808417-74946455	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74894400-74908200	Weak transcription	GM12878-XiMat	blood
2	chr5:74906200-74907400	Bivalent Enhancer	Fetal Heart	heart
3	chr5:74906600-74907800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr5:74906600-74907800	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr5:74906600-74908200	Active TSS	A549	lung
6	chr5:74906800-74907400	Enhancers	K562	blood
7	chr5:74906800-74907800	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr5:74906800-74908000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr5:74906800-74908000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr5:74906800-74908000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:74906800-74908000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:74906800-74908000	Flanking Active TSS	Liver	Liver
13	chr5:74906800-74908000	Active TSS	Brain Angular Gyrus	brain
14	chr5:74906800-74908000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:74906800-74908000	Active TSS	Brain Substantia Nigra	brain
16	chr5:74906800-74908000	Active TSS	Stomach Mucosa	stomach
17	chr5:74906800-74908200	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr5:74906800-74908200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr5:74906800-74908200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:74906800-74908200	Active TSS	Brain Anterior Caudate	brain
21	chr5:74906800-74908200	Active TSS	Fetal Brain Female	brain
22	chr5:74906800-74908200	Active TSS	Fetal Kidney	kidney
23	chr5:74906800-74908200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr5:74906800-74908200	Active TSS	Fetal Lung	lung
25	chr5:74906800-74908200	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr5:74906800-74908400	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr5:74906800-74908400	Active TSS	Duodenum Mucosa	Duodenum
28	chr5:74906800-74908400	Active TSS	Rectal Smooth Muscle	rectum
29	chr5:74906800-74908600	Active TSS	Fetal Intestine Small	intestine
30	chr5:74906800-74909000	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr5:74907000-74907400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr5:74907000-74907400	Active TSS	Primary hematopoietic stem cells	blood
33	chr5:74907000-74907400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
34	chr5:74907000-74907400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:74907000-74907400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr5:74907000-74907400	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr5:74907000-74907400	Flanking Active TSS	Pancreas	Pancrea
38	chr5:74907000-74907600	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
39	chr5:74907000-74907600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
40	chr5:74907000-74907600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:74907000-74907800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:74907000-74907800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:74907000-74907800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:74907000-74907800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:74907000-74907800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr5:74907000-74907800	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr5:74907000-74907800	Active TSS	Gastric	stomach
48	chr5:74907000-74907800	Flanking Active TSS	Right Atrium	heart
49	chr5:74907000-74908000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr5:74907000-74908000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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