Variant report

Variant	rs1504980
Chromosome Location	chr5:118623391-118623392
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	chr5:118622873..118625111-chr5:118638258..118641948,4	MCF-7	breast:
2	chr5:118622239..118624892-chr5:118626281..118628350,2	MCF-7	breast:
3	chr5:118604065..118607023-chr5:118622337..118626495,5	MCF-7	breast:
4	chr5:118622285..118624506-chr5:118651501..118653957,2	MCF-7	breast:
5	chr5:118609964..118611606-chr5:118621803..118623586,2	MCF-7	breast:
6	chr5:118623079..118625774-chr5:118657977..118661910,3	MCF-7	breast:
7	chr5:118617115..118620555-chr5:118621915..118624851,4	MCF-7	breast:
8	chr5:118623266..118625582-chr5:118625738..118628697,2	MCF-7	breast:
9	chr5:118602857..118608494-chr5:118621291..118626100,9	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000145779	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10035514	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10053596	0.80[CEU][hapmap]
rs10063063	1.00[EUR][1000 genomes]
rs1032859	0.93[EUR][1000 genomes]
rs1035376	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10519579	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13153732	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13172935	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1394630	0.85[CHB][hapmap]
rs1422012	0.83[ASN][1000 genomes]
rs1504979	0.83[ASN][1000 genomes]
rs17145063	1.00[JPT][hapmap]
rs17145066	1.00[JPT][hapmap]
rs17145124	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17145129	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs17145142	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2112323	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs6876958	0.88[CEU][hapmap];0.98[EUR][1000 genomes]
rs6877317	0.83[ASN][1000 genomes]
rs6878373	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6879919	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs72786107	0.84[ASN][1000 genomes]
rs73248910	0.88[ASN][1000 genomes]
rs888768	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888771	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs888772	1.00[CEU][hapmap];1.00[EUR][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	esv2757136	chr5:118555863-118667748	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription 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 target site	19 gene(s)	inside rSNPs	diseases
2	esv2759374	chr5:118555863-118667748	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1024648	chr5:118608175-118678268	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv869828	chr5:118610548-118691190	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118610800-118626000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr5:118611200-118625200	Weak transcription	Right Atrium	heart
3	chr5:118612000-118625200	Weak transcription	Fetal Muscle Leg	muscle
4	chr5:118613200-118623400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:118613800-118626000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:118614000-118623400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:118615000-118626200	Weak transcription	Spleen	Spleen
8	chr5:118616800-118624600	Enhancers	Fetal Heart	heart
9	chr5:118618400-118627800	Weak transcription	Right Ventricle	heart
10	chr5:118618800-118623800	Weak transcription	Fetal Kidney	kidney
11	chr5:118619400-118628600	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr5:118619800-118629600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr5:118620000-118625200	Weak transcription	Gastric	stomach
14	chr5:118620000-118629400	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr5:118620600-118623600	Weak transcription	Aorta	Aorta
16	chr5:118620800-118623600	Enhancers	Adipose Nuclei	Adipose
17	chr5:118620800-118624800	Enhancers	Osteobl	bone
18	chr5:118620800-118625200	Enhancers	NH-A	brain
19	chr5:118621000-118623600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr5:118621000-118625800	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr5:118621200-118624600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr5:118621400-118623400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:118621400-118623400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr5:118621400-118623400	Enhancers	K562	blood
25	chr5:118621400-118623600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:118621400-118627000	Weak transcription	Fetal Brain Female	brain
27	chr5:118621600-118623400	Weak transcription	HSMMtube	muscle
28	chr5:118621800-118623400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr5:118621800-118623400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:118621800-118625400	Flanking Active TSS	Dnd41	blood
31	chr5:118621800-118626600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr5:118621800-118627400	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr5:118622000-118624800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:118622200-118623400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:118622200-118623400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr5:118622200-118623800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr5:118622200-118628200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:118622400-118623400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:118622400-118623400	Enhancers	Pancreas	Pancrea
40	chr5:118622400-118623800	Flanking Active TSS	Hela-S3	cervix
41	chr5:118622400-118624400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr5:118622400-118626600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:118622400-118626600	Flanking Active TSS	GM12878-XiMat	blood
44	chr5:118622400-118628000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr5:118622400-118628000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr5:118622600-118623400	Enhancers	HMEC	breast
47	chr5:118622600-118624000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:118622600-118624000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:118622600-118624000	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr5:118622600-118624800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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