Variant report

Variant	rs6601280
Chromosome Location	chr8:8909236-8909237
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:8907031..8909289-chr8:9008104..9009866,2	K562	blood:
2	chr8:8895603..8897161-chr8:8907687..8909459,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173281	Chromatin interaction
ENSG00000253426	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10105813	1.00[CHB][hapmap]
rs10217044	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1045527	0.92[CEU][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1045529	0.85[CEU][hapmap]
rs11784393	0.92[CEU][hapmap]
rs11785634	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11785819	0.92[CEU][hapmap];0.84[AMR][1000 genomes]
rs11787026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12114954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13252797	0.92[CEU][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs13271797	0.92[CEU][hapmap];0.81[LWK][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1562211	0.92[CEU][hapmap]
rs17702602	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288671	0.82[CEU][hapmap]
rs2409120	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28482034	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28665409	0.80[AMR][1000 genomes]
rs2915251	0.82[CEU][hapmap]
rs2956244	0.84[CEU][hapmap]
rs2979247	0.82[CEU][hapmap]
rs2979256	0.81[CEU][hapmap]
rs2979265	0.82[CEU][hapmap]
rs34004903	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34251783	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3855900	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3895823	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3989373	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4840389	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4841083	0.84[CEU][hapmap]
rs6601279	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6601281	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601282	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs6748	0.92[CEU][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6981060	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6983877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6986044	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6987107	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6987558	0.82[CEU][hapmap]
rs7005056	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7005133	0.92[CEU][hapmap]
rs7009435	1.00[CHB][hapmap]
rs7014430	0.83[CEU][hapmap]
rs7017868	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7462373	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7814328	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9329175	0.88[CEU][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes]
rs9650616	0.92[CEU][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv831229	chr8:8751523-8926235	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6601280	C8orf13	cis	multi-tissue	Pritchard
rs6601280	THEX1	Cis_1M	lymphoblastoid	RTeQTL
rs6601280	SGK223	cis	Thyroid	GTEx
rs6601280	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs6601280	RP11-62H7.2	cis	Thyroid	GTEx
rs6601280	CLDN23	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8861800-8915600	Weak transcription	Pancreas	Pancrea
2	chr8:8888400-8910800	Weak transcription	Hela-S3	cervix
3	chr8:8891000-8914800	Weak transcription	Fetal Stomach	stomach
4	chr8:8891400-8915200	Weak transcription	K562	blood
5	chr8:8893800-8913800	Weak transcription	Primary T cells from cord blood	blood
6	chr8:8899000-8919200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr8:8903200-8910200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr8:8905600-8910800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr8:8905800-8911000	Weak transcription	Fetal Lung	lung
10	chr8:8906200-8913000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr8:8906200-8914600	Weak transcription	Fetal Muscle Leg	muscle
12	chr8:8907200-8909400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr8:8907400-8910800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr8:8907400-8915000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr8:8907600-8910800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr8:8907600-8913400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr8:8907600-8914800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr8:8907600-8915000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr8:8908600-8914800	Weak transcription	NHDF-Ad	bronchial
20	chr8:8909000-8914800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr8:8909200-8909400	Enhancers	HMEC	breast
22	chr8:8909200-8910000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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