Variant report

Variant	rs2409040
Chromosome Location	chr5:127291878-127291879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127290516..127294335-chr5:127417480..127422773,4	MCF-7	breast:
2	chr5:127291358..127294527-chr5:127295144..127299558,4	K562	blood:

Variant related genes	Relation type
ENSG00000064651	Chromatin interaction
ENSG00000245937	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10040931	0.89[EUR][1000 genomes]
rs10041355	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10041388	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10052149	0.80[EUR][1000 genomes]
rs10055964	0.82[EUR][1000 genomes]
rs10057048	0.80[EUR][1000 genomes]
rs1013374	0.88[EUR][1000 genomes]
rs1013375	0.88[EUR][1000 genomes]
rs10478786	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10478787	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10478788	0.80[EUR][1000 genomes]
rs11745009	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11745023	0.89[EUR][1000 genomes]
rs12523625	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13174053	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13177354	0.82[EUR][1000 genomes]
rs13180050	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1558149	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17606751	0.82[EUR][1000 genomes]
rs2041143	0.80[EUR][1000 genomes]
rs2108652	0.80[EUR][1000 genomes]
rs2108654	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2159110	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2409038	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2409039	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2898077	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4835934	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59634534	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6881456	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6889393	0.80[EUR][1000 genomes]
rs6892704	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732235	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732236	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs768528	0.88[EUR][1000 genomes]
rs7713606	0.88[EUR][1000 genomes]
rs7717705	0.87[EUR][1000 genomes]
rs7722601	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127267400-127292200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:127269800-127292400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:127271200-127294800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:127274800-127295000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:127274800-127296000	Weak transcription	Primary B cells from cord blood	blood
6	chr5:127278400-127292800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:127278400-127292800	Weak transcription	Brain Substantia Nigra	brain
8	chr5:127278400-127292800	Weak transcription	HSMM	muscle
9	chr5:127278400-127294600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr5:127278400-127295600	Weak transcription	HSMMtube	muscle
11	chr5:127280200-127292800	Weak transcription	Gastric	stomach
12	chr5:127281800-127295400	Weak transcription	Psoas Muscle	Psoas
13	chr5:127285200-127295200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr5:127285800-127303800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:127286600-127295200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:127286800-127292600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:127287000-127292200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr5:127287000-127292600	Weak transcription	Fetal Intestine Small	intestine
19	chr5:127287400-127293000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:127287400-127297200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr5:127287600-127292800	Weak transcription	Colon Smooth Muscle	Colon
22	chr5:127288000-127292200	Weak transcription	A549	lung
23	chr5:127288200-127295200	Weak transcription	Primary T cells from cord blood	blood
24	chr5:127289000-127294600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:127290400-127294600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr5:127290600-127332000	Weak transcription	Aorta	Aorta
27	chr5:127290800-127292800	Weak transcription	Right Ventricle	heart
28	chr5:127290800-127295400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:127290800-127297400	Weak transcription	Spleen	Spleen
30	chr5:127291600-127295000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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