Variant report

Variant	rs6877849
Chromosome Location	chr5:60088619-60088620
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	chr5:60087441..60089276-chr5:60089305..60090863,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10057395	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10062839	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10072745	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10076679	0.87[ASN][1000 genomes]
rs10077663	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10939874	1.00[CEU][hapmap]
rs12696975	0.80[EUR][1000 genomes]
rs13153359	0.81[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs13184554	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13186761	0.82[EUR][1000 genomes]
rs13358053	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs1445292	0.89[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1445293	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs158916	1.00[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs158920	1.00[CEU][hapmap]
rs158928	1.00[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs1609041	1.00[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs16878397	0.81[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1824531	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1870015	0.91[ASN][1000 genomes]
rs2306350	1.00[CEU][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs2306351	1.00[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs35006499	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36111624	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3936423	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4235481	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4235482	0.87[ASN][1000 genomes]
rs4410607	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4479795	0.87[AMR][1000 genomes]
rs4482855	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4647078	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs4647108	1.00[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs4647168	1.00[CEU][hapmap]
rs4700392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4700393	0.91[ASN][1000 genomes]
rs4700394	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs4700398	0.83[CHD][hapmap]
rs55809585	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6449500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6449501	0.87[ASN][1000 genomes]
rs6449502	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6449503	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6449504	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6449505	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs6449509	1.00[CEU][hapmap]
rs6449510	1.00[CEU][hapmap]
rs6869332	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6871557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6872863	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6873181	0.91[ASN][1000 genomes]
rs6875456	0.87[ASN][1000 genomes]
rs6876335	0.87[ASN][1000 genomes]
rs6876346	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6877757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6889730	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6890201	0.87[ASN][1000 genomes]
rs6893642	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6894672	0.91[ASN][1000 genomes]
rs6894750	0.87[ASN][1000 genomes]
rs6894795	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs702564	0.88[GIH][hapmap];0.96[TSI][hapmap]
rs7445953	0.90[CEU][hapmap]
rs7712473	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7714071	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7730827	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7731760	0.84[CEU][hapmap]
rs921897	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers 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
2	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv934153	chr5:60004982-60309751	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv2763456	chr5:60007355-60151767	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv1026190	chr5:60020156-60148535	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv537769	chr5:60020156-60148535	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv2752073	chr5:60034475-60136626	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	42 gene(s)	inside rSNPs	diseases
10	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6877849	ERCC8	cis	multi-tissue	Pritchard
rs6877849	NDUFAF2	cis	cerebellum	SCAN
rs6877849	CWC27	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60044800-60098000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:60057600-60092200	Weak transcription	Brain Anterior Caudate	brain
3	chr5:60057600-60093200	Weak transcription	Pancreas	Pancrea
4	chr5:60065200-60091800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:60065200-60101200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:60075400-60092800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:60075400-60093000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:60075800-60090800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:60077400-60092000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:60077400-60092000	Weak transcription	Brain Substantia Nigra	brain
11	chr5:60080200-60101400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:60082000-60092200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:60082000-60092400	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:60082400-60090000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:60082400-60112600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:60085400-60089800	Weak transcription	Fetal Intestine Small	intestine
17	chr5:60085400-60090200	Weak transcription	Fetal Intestine Large	intestine
18	chr5:60085600-60090000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr5:60088600-60091000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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