Variant report

Variant	rs2731878
Chromosome Location	chr5:36602563-36602564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:36602536..36603410-chr5:36692728..36693815,5	MCF-7	breast:
2	chr5:36602557..36603415-chr5:36695863..36696651,3	MCF-7	breast:
3	chr5:36598036..36602737-chr5:36604248..36607271,4	K562	blood:

Variant related genes	Relation type
ENSG00000079215	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10078147	0.92[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs13436644	0.92[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs1428972	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2562575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2562576	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562577	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2562578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2562579	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2562580	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2562581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2731879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2731883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2731884	1.00[CEU][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2731886	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3814068	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4591778	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7730144	0.96[YRI][hapmap]

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	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv881025	chr5:36575021-36613053	Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
3	nsv830263	chr5:36576504-36755093	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2762516	chr5:36599385-36613201	Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36591200-36606200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:36597000-36603000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:36597000-36605600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:36597000-36606200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:36597200-36605200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:36598200-36603000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:36598200-36603000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:36598400-36603000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:36598400-36603200	Weak transcription	Fetal Muscle Leg	muscle
10	chr5:36598400-36604400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:36600000-36604200	Enhancers	Brain Angular Gyrus	brain
12	chr5:36600000-36605600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:36600200-36602600	Enhancers	Brain Germinal Matrix	brain
14	chr5:36600200-36605600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr5:36600200-36606000	Enhancers	Brain Substantia Nigra	brain
16	chr5:36600800-36603000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:36601000-36604600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:36601000-36605000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:36601000-36605800	Weak transcription	Adipose Nuclei	Adipose
20	chr5:36601200-36605400	Weak transcription	NHEK	skin
21	chr5:36601200-36605600	Weak transcription	HMEC	breast
22	chr5:36601200-36605800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:36601200-36606000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:36601400-36605200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:36601600-36604800	Weak transcription	NHDF-Ad	bronchial
26	chr5:36601800-36604200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:36601800-36605200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:36601800-36605200	Enhancers	Brain Hippocampus Middle	brain
29	chr5:36601800-36605800	Weak transcription	Fetal Stomach	stomach
30	chr5:36601800-36606000	Weak transcription	NHLF	lung
31	chr5:36602000-36606200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:36602200-36602600	Weak transcription	Brain Anterior Caudate	brain
33	chr5:36602200-36603200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:36602200-36605400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:36602200-36605800	Weak transcription	Fetal Brain Female	brain
36	chr5:36602200-36606200	Weak transcription	Pancreas	Pancrea
37	chr5:36602400-36602800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr5:36602400-36602800	Weak transcription	Brain Inferior Temporal Lobe	brain

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