Variant report

Variant	rs876954
Chromosome Location	chr8:8310923-8310924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:8297402..8302075-chr8:8309900..8314859,7	MCF-7	breast:
2	chr8:8306469..8311532-chr8:8316315..8320180,6	MCF-7	breast:
3	chr8:8237866..8240823-chr8:8310722..8313327,2	MCF-7	breast:
4	chr8:8307359..8308990-chr8:8310543..8313387,3	MCF-7	breast:
5	chr8:8310535..8312786-chr8:8315430..8317371,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254153	Chromatin interaction
ENSG00000182319	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs2921051	0.80[AMR][1000 genomes]
rs2921053	0.84[AMR][1000 genomes]
rs2921055	0.86[CHB][hapmap]
rs2921057	0.87[AMR][1000 genomes]
rs2921060	0.81[ASW][hapmap];0.86[CHB][hapmap];0.89[MEX][hapmap]
rs2921061	0.81[AMR][1000 genomes]
rs2921077	0.85[EUR][1000 genomes]
rs2921080	0.83[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2921081	0.80[ASN][1000 genomes]
rs2921084	0.82[JPT][hapmap]
rs2945861	0.82[JPT][hapmap]
rs2976855	0.80[EUR][1000 genomes]
rs2976856	0.82[JPT][hapmap]
rs2976860	0.82[JPT][hapmap]
rs2976876	0.86[CHB][hapmap];0.89[MEX][hapmap]
rs2976893	0.80[AMR][1000 genomes]
rs2976902	0.84[AMR][1000 genomes]
rs2976906	0.84[AMR][1000 genomes]
rs2976907	0.94[YRI][hapmap]
rs2976909	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs2976935	0.82[JPT][hapmap]
rs2979172	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2979179	0.86[CHB][hapmap];0.89[MEX][hapmap]
rs2979181	1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2979202	0.81[AMR][1000 genomes]
rs2979230	0.80[ASN][1000 genomes]
rs2980766	0.80[AMR][1000 genomes]
rs7817376	0.94[MEX][hapmap]
rs7827182	0.89[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 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	nsv465448	chr8:8098079-8403142	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv610152	chr8:8098079-8403142	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv610153	chr8:8098079-8454531	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv610154	chr8:8101641-8328101	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1025994	chr8:8108863-8580201	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1029268	chr8:8130629-8403435	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv539446	chr8:8130629-8403435	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv831227	chr8:8204838-8367160	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
13	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
14	nsv1019613	chr8:8239352-8636357	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
15	nsv539452	chr8:8239352-8636357	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	nsv465449	chr8:8262897-8362710	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv610158	chr8:8262897-8362710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv465451	chr8:8273043-8311298	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv610159	chr8:8273043-8311298	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv610171	chr8:8290294-8328101	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv1025136	chr8:8290818-8326308	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1034903	chr8:8295208-8324479	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv539454	chr8:8295208-8324479	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv519143	chr8:8296071-8328101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs876954	FAM86B3P	cis	Esophagus Mucosa	GTEx
rs876954	PPP1R3B	cis	cerebellum	SCAN
rs876954	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs876954	PRSS55	cis	cerebellum	SCAN
rs876954	DEFB134	cis	cerebellum	SCAN
rs876954	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs876954	FLJ10661	cis	parietal	SCAN
rs876954	CTSB	cis	cerebellum	SCAN
rs876954	SGK223	cis	Thyroid	GTEx
rs876954	MFHAS1	cis	cerebellum	SCAN
rs876954	CTA-398F10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs876954	FLJ10661	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8307200-8311600	Enhancers	Primary B cells from peripheral blood	blood
2	chr8:8308800-8311000	Enhancers	GM12878-XiMat	blood
3	chr8:8309000-8311400	Enhancers	Primary B cells from cord blood	blood
4	chr8:8309000-8313200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr8:8309600-8311400	Enhancers	Fetal Brain Male	brain
6	chr8:8310200-8311000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr8:8310200-8311000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr8:8310200-8311000	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr8:8310200-8311000	Enhancers	Fetal Brain Female	brain
10	chr8:8310400-8311000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr8:8310400-8311000	Enhancers	A549	lung
12	chr8:8310600-8311000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr8:8310600-8311000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr8:8310600-8312200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr8:8310800-8311000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr8:8310800-8312200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr8:8310800-8312400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr8:8310800-8312400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:8310800-8312400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:8310800-8313400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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