Variant report

Variant	rs827528
Chromosome Location	chr8:104312432-104312433
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr8:104312297-104312478	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr8:104311800-104312770	SK-N-SH	brain:	n/a	n/a
3	MAX	chr8:104310525-104312693	MCF-7	breast:	n/a	chr8:104312304-104312315
4	FOS	chr8:104312146-104312665	MCF10A-Er-Src	breast:	n/a	n/a
5	JUND	chr8:104311916-104312679	SK-N-SH	brain:	n/a	chr8:104312290-104312301
6	STAT3	chr8:104312195-104312532	MCF10A-Er-Src	breast:	n/a	chr8:104312320-104312328 chr8:104312240-104312248
7	MXI1	chr8:104311420-104312499	Hela-S3	cervix:	n/a	n/a
8	MYC	chr8:104312257-104312519	MCF10A-Er-Src	breast:	n/a	chr8:104312304-104312315
9	POLR2A	chr8:104310494-104312668	IMR90	lung:	n/a	n/a
10	BRCA1	chr8:104310445-104312598	Hela-S3	cervix:	n/a	chr8:104311074-104311083
11	TCF12	chr8:104311832-104312789	SK-N-SH	brain:	n/a	n/a
12	YY1	chr8:104312179-104312629	SK-N-SH	brain:	n/a	n/a
13	ZNF263	chr8:104311042-104312484	HEK293-T-REx	kidney:	n/a	n/a
14	STAT3	chr8:104312291-104312476	MCF10A-Er-Src	breast:	n/a	chr8:104312320-104312328
15	POLR2A	chr8:104312256-104312479	SK-N-SH	brain:	n/a	n/a
16	GATA3	chr8:104311845-104312644	SK-N-SH	brain:	n/a	n/a
17	FOS	chr8:104312124-104312615	MCF10A-Er-Src	breast:	n/a	n/a
18	FOSL2	chr8:104311954-104312648	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr8:104309707-104313471	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr8:104311427-104312478	SK-N-SH	brain:	n/a	n/a
21	E2F4	chr8:104312402-104312658	MCF10A-Er-Src	breast:	n/a	n/a
22	MYC	chr8:104311459-104312615	MCF10A-Er-Src	breast:	n/a	chr8:104312304-104312315
23	FOS	chr8:104312157-104312586	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr8:104312219-104313349	MCF10A-Er-Src	breast:	n/a	n/a
25	STAT3	chr8:104311996-104312710	MCF10A-Er-Src	breast:	n/a	chr8:104312320-104312328 chr8:104312240-104312248

No.	Distal block	Cell Line	Cell type
1	chr8:104311011..104313390-chr8:104387809..104389665,2	MCF-7	breast:
2	chr8:104310872..104313669-chr8:104425556..104428778,5	MCF-7	breast:
3	chr1:156736343..156738985-chr8:104309679..104312476,2	MCF-7	breast:
4	chr8:104309661..104313454-chr8:104382208..104385836,8	MCF-7	breast:
5	chr3:101567790..101569895-chr8:104310812..104313002,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247081	TF binding region
ENSG00000164933	Chromatin interaction
ENSG00000144802	Chromatin interaction
ENSG00000164932	Chromatin interaction
ENSG00000143321	Chromatin interaction
ENSG00000164934	Chromatin interaction
ENSG00000143294	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10089343	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10090069	0.83[ASN][1000 genomes]
rs10094939	1.00[CHB][hapmap]
rs10096207	0.83[ASN][1000 genomes]
rs10097121	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10101517	0.83[ASN][1000 genomes]
rs10102413	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10103739	0.83[ASN][1000 genomes]
rs10105195	0.83[ASN][1000 genomes]
rs10105450	0.83[ASN][1000 genomes]
rs10106795	1.00[ASN][1000 genomes]
rs10109642	0.83[ASN][1000 genomes]
rs10112450	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10112941	0.83[ASN][1000 genomes]
rs10112952	0.83[ASN][1000 genomes]
rs10113160	0.83[ASN][1000 genomes]
rs10113367	0.83[ASN][1000 genomes]
rs1032471	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1061196	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1095715	0.84[EUR][1000 genomes]
rs11779349	1.00[ASN][1000 genomes]
rs11781628	1.00[CHB][hapmap]
rs11785583	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11985002	0.83[ASN][1000 genomes]
rs12707777	1.00[ASN][1000 genomes]
rs13255562	0.83[ASN][1000 genomes]
rs13257958	0.83[ASN][1000 genomes]
rs13258345	1.00[ASN][1000 genomes]
rs13263611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13266347	0.83[ASN][1000 genomes]
rs13266642	0.83[ASN][1000 genomes]
rs13273192	1.00[ASN][1000 genomes]
rs13278335	0.83[ASN][1000 genomes]
rs13282967	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13439041	1.00[CHD][hapmap]
rs1370007	1.00[CHB][hapmap]
rs1403294	0.91[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17205821	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17228538	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17802416	1.00[CHB][hapmap]
rs17802518	0.83[ASN][1000 genomes]
rs17804088	1.00[CHB][hapmap]
rs17804149	1.00[CHB][hapmap]
rs2642365	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2642369	0.84[EUR][1000 genomes]
rs28437723	0.83[ASN][1000 genomes]
rs28811720	0.83[ASN][1000 genomes]
rs28862349	0.83[ASN][1000 genomes]
rs2948449	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3104026	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34208282	1.00[ASN][1000 genomes]
rs35225263	0.83[ASN][1000 genomes]
rs35392014	0.83[ASN][1000 genomes]
rs57237927	0.83[ASN][1000 genomes]
rs6468866	1.00[ASN][1000 genomes]
rs6985718	0.83[ASN][1000 genomes]
rs6989714	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6990501	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs71520811	0.83[ASN][1000 genomes]
rs71520812	0.83[ASN][1000 genomes]
rs72675443	0.83[ASN][1000 genomes]
rs72675444	0.83[ASN][1000 genomes]
rs72675445	0.83[ASN][1000 genomes]
rs7464317	1.00[ASN][1000 genomes]
rs7820626	0.83[ASN][1000 genomes]
rs7839421	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7845210	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs827526	0.87[CEU][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs827537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827538	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs827540	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs827546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951826	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs973242	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs981816	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1848810	chr8:104128496-104369288	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	esv1844303	chr8:104128696-104369090	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1015965	chr8:104192086-104361108	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1017326	chr8:104236193-104313235	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1023181	chr8:104298542-104366365	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1020476	chr8:104312212-104924482	Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv539704	chr8:104312212-104924482	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs827528	FZD6	cis	brain	BrainEAC
rs827528	DCAF13	cis	cerebellum	SCAN
rs827528	FZD6	cis	parietal	SCAN
rs827528	FZD6	cis	cerebellum	SCAN
rs827528	FZD6	cis	occipital cortex	BrainEAC
rs827528	FZD6	Cis_1M	lymphoblastoid	RTeQTL
rs827528	LRP12	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104308600-104313800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:104310000-104313400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr8:104310000-104313800	Active TSS	Aorta	Aorta
4	chr8:104310200-104312600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr8:104310200-104312800	Active TSS	Stomach Smooth Muscle	stomach
6	chr8:104310400-104313000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr8:104310400-104313400	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr8:104310600-104312600	Active TSS	Brain Angular Gyrus	brain
9	chr8:104310600-104313200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr8:104310800-104313000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr8:104311400-104312600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr8:104311400-104313400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr8:104311400-104313600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr8:104311600-104312600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr8:104311600-104312600	Active TSS	Psoas Muscle	Psoas
16	chr8:104311600-104312600	Active TSS	Right Atrium	heart
17	chr8:104311600-104312600	Flanking Active TSS	Dnd41	blood
18	chr8:104311600-104312600	Flanking Active TSS	NH-A	brain
19	chr8:104311600-104313200	Flanking Active TSS	HUVEC	blood vessel
20	chr8:104311600-104343600	Weak transcription	Spleen	Spleen
21	chr8:104311800-104312600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
22	chr8:104311800-104312600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr8:104311800-104312600	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr8:104311800-104312600	Flanking Active TSS	Fetal Heart	heart
25	chr8:104311800-104312600	Flanking Active TSS	HepG2	liver
26	chr8:104311800-104312600	Flanking Active TSS	NHLF	lung
27	chr8:104311800-104313400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr8:104311800-104313600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr8:104311800-104320000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr8:104311800-104320200	Weak transcription	Placenta	Placenta
31	chr8:104311800-104320200	Weak transcription	HSMM	muscle
32	chr8:104311800-104321200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr8:104311800-104327800	Weak transcription	Pancreas	Pancrea
34	chr8:104311800-104331200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr8:104311800-104331400	Weak transcription	Liver	Liver
36	chr8:104311800-104331400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr8:104311800-104343600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr8:104312000-104312600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr8:104312000-104312600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr8:104312000-104312600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr8:104312000-104312600	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr8:104312000-104312600	Enhancers	Fetal Intestine Small	intestine
43	chr8:104312000-104312600	Flanking Active TSS	Hela-S3	cervix
44	chr8:104312000-104312600	Flanking Active TSS	NHEK	skin
45	chr8:104312000-104313000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr8:104312000-104313400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr8:104312000-104316400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr8:104312000-104326600	Weak transcription	Gastric	stomach
49	chr8:104312000-104337200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr8:104312000-104337200	Weak transcription	Brain Inferior Temporal Lobe	brain

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