Variant report

Variant	rs2270525
Chromosome Location	chr8:104340719-104340720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:104332096..104335795-chr8:104338249..104342191,4	MCF-7	breast:
2	chr8:104332978..104337328-chr8:104338203..104342176,5	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12541167	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs12543038	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs13275377	0.83[AMR][1000 genomes]
rs13278361	0.83[AMR][1000 genomes]
rs1353212	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1353213	1.00[ASW][hapmap];0.88[CEU][hapmap];0.84[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1403293	0.88[AMR][1000 genomes]
rs1464551	0.93[ASN][1000 genomes]
rs1494278	0.83[AMR][1000 genomes]
rs1522707	0.86[CHB][hapmap];0.81[AMR][1000 genomes]
rs1522713	0.89[CEU][hapmap];0.95[AMR][1000 genomes]
rs1568641	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16870243	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs16870245	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs16870249	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17205332	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs1965482	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1982892	0.83[AMR][1000 genomes]
rs1982893	0.83[AMR][1000 genomes]
rs2131860	0.89[CEU][hapmap];0.94[MEX][hapmap];0.95[AMR][1000 genomes]
rs2220825	0.88[CEU][hapmap];0.84[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3104029	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3104031	0.88[AMR][1000 genomes]
rs3107646	0.86[CHB][hapmap]
rs3107648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3107649	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3116457	0.85[AMR][1000 genomes]
rs3116462	0.95[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3116464	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3116466	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3116468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3133820	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3133821	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3133824	0.83[AMR][1000 genomes]
rs3133825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3133830	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3133832	0.98[ASN][1000 genomes]
rs3133834	1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[ASN][1000 genomes]
rs3133835	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs3133836	1.00[ASW][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs34185273	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34201011	0.83[AMR][1000 genomes]
rs34273148	0.83[AMR][1000 genomes]
rs34337822	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs827577	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

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	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
6	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
7	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
8	nsv1016395	chr8:104327541-104473005	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2270525	FZD6	cis	cerebellum	SCAN
rs2270525	SLC25A32	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104311600-104343600	Weak transcription	Spleen	Spleen
2	chr8:104311800-104343600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:104312000-104343800	Weak transcription	Small Intestine	intestine
4	chr8:104312000-104348400	Weak transcription	Thymus	Thymus
5	chr8:104312000-104350200	Weak transcription	Esophagus	oesophagus
6	chr8:104312400-104345000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr8:104312400-104345000	Weak transcription	Right Ventricle	heart
8	chr8:104312400-104350000	Weak transcription	Lung	lung
9	chr8:104312600-104342400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr8:104312600-104344800	Weak transcription	Fetal Intestine Small	intestine
11	chr8:104312600-104350000	Weak transcription	Colon Smooth Muscle	Colon
12	chr8:104317400-104354000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr8:104317600-104345800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr8:104318000-104345200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr8:104318200-104342600	Weak transcription	Brain Substantia Nigra	brain
16	chr8:104318600-104343400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr8:104319400-104347200	Weak transcription	Hela-S3	cervix
18	chr8:104320400-104343600	Weak transcription	Fetal Intestine Large	intestine
19	chr8:104321400-104342000	Weak transcription	Placenta	Placenta
20	chr8:104321400-104358800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr8:104321600-104350200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr8:104322800-104350200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr8:104324800-104348200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr8:104325800-104342000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr8:104327800-104342000	Weak transcription	HSMM	muscle
26	chr8:104327800-104344800	Weak transcription	A549	lung
27	chr8:104328200-104344600	Weak transcription	HepG2	liver
28	chr8:104328200-104355800	Weak transcription	Gastric	stomach
29	chr8:104328200-104361200	Weak transcription	Pancreas	Pancrea
30	chr8:104328800-104345600	Weak transcription	Fetal Heart	heart
31	chr8:104330400-104350200	Weak transcription	Psoas Muscle	Psoas
32	chr8:104331800-104347200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr8:104331800-104352000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr8:104332000-104348200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr8:104332600-104342000	Weak transcription	Ovary	ovary
36	chr8:104333000-104342000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr8:104333000-104342000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr8:104333000-104344800	Weak transcription	Fetal Stomach	stomach
39	chr8:104334200-104342000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr8:104334200-104347000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr8:104334200-104348800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr8:104335800-104347800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr8:104336600-104348400	Weak transcription	GM12878-XiMat	blood
44	chr8:104337400-104344400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr8:104337400-104344400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr8:104337600-104341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr8:104337600-104341800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr8:104337600-104342000	Weak transcription	Dnd41	blood
49	chr8:104337600-104348600	Weak transcription	HSMMtube	muscle
50	chr8:104337800-104341800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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