Variant report

Variant	rs6449525
Chromosome Location	chr5:60590591-60590592
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	chr5:60586340..60593423-chr5:60595007..60600646,11	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10939897	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs10939900	0.81[GIH][hapmap]
rs11743133	0.83[EUR][1000 genomes]
rs11747144	0.86[CEU][hapmap]
rs13154581	0.82[EUR][1000 genomes]
rs13154663	0.81[CEU][hapmap];0.87[CHD][hapmap];0.83[EUR][1000 genomes]
rs13162866	0.87[CEU][hapmap]
rs13164720	0.87[CEU][hapmap]
rs13171223	0.82[EUR][1000 genomes]
rs13174916	0.81[EUR][1000 genomes]
rs13181015	0.81[GIH][hapmap]
rs4132385	0.81[ASN][1000 genomes]
rs4235486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4391122	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4409043	0.81[EUR][1000 genomes]
rs4421060	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4513641	0.87[CEU][hapmap];0.87[CHD][hapmap];0.81[EUR][1000 genomes]
rs4544785	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs4546329	0.93[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4583848	0.95[ASN][1000 genomes]
rs62366236	0.81[EUR][1000 genomes]
rs6449526	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449527	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449530	0.81[GIH][hapmap]
rs6860599	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860608	0.81[GIH][hapmap]
rs6867278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6870349	0.81[CEU][hapmap];0.87[CHD][hapmap]
rs6881765	0.81[GIH][hapmap];0.80[TSI][hapmap]
rs6889338	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7704636	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60573400-60594800	Weak transcription	Right Atrium	heart
2	chr5:60587000-60594000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:60587000-60594600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:60587000-60595200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:60587000-60597400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:60587200-60593800	Weak transcription	A549	lung
7	chr5:60587200-60594000	Weak transcription	NHDF-Ad	bronchial
8	chr5:60587200-60595000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:60587200-60597200	Weak transcription	Brain Hippocampus Middle	brain
10	chr5:60587200-60597400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:60587400-60591800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:60587400-60591800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:60587400-60594200	Weak transcription	Osteobl	bone
14	chr5:60587400-60594400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:60587400-60594600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr5:60587400-60595200	Weak transcription	HSMM	muscle
17	chr5:60587600-60591600	Weak transcription	NHLF	lung
18	chr5:60588200-60591400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:60589200-60590600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:60589200-60590600	Weak transcription	Gastric	stomach
21	chr5:60589200-60594000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:60589200-60594000	Weak transcription	NHEK	skin
23	chr5:60589200-60594400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:60589200-60594600	Weak transcription	Esophagus	oesophagus
25	chr5:60589200-60594600	Weak transcription	Lung	lung
26	chr5:60589200-60597200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr5:60589400-60592000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:60589400-60594000	Weak transcription	Pancreas	Pancrea
29	chr5:60589400-60597000	Weak transcription	Fetal Intestine Large	intestine
30	chr5:60589400-60597400	Weak transcription	Brain Anterior Caudate	brain
31	chr5:60589600-60594000	Weak transcription	Stomach Mucosa	stomach
32	chr5:60590400-60592400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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