Variant report

Variant	rs565720
Chromosome Location	chr8:103914366-103914367
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:103910864..103914937-chr8:103922491..103926362,4	MCF-7	breast:
2	chr8:103909625..103914681-chr8:103915019..103918768,8	MCF-7	breast:
3	chr8:103903842..103907470-chr8:103913570..103917002,5	MCF-7	breast:
4	chr8:103913695..103915719-chr8:103927933..103930318,2	MCF-7	breast:
5	chr8:103903395..103905435-chr8:103912385..103915123,2	MCF-7	breast:
6	chr8:103886724..103888793-chr8:103913396..103915267,2	MCF-7	breast:
7	chr8:103874072..103879942-chr8:103913926..103921009,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253263	Chromatin interaction
ENSG00000253320	Chromatin interaction
ENSG00000155096	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1019976	0.88[CHB][hapmap]
rs1055376	0.87[CHD][hapmap];0.83[GIH][hapmap];0.86[YRI][hapmap]
rs1062048	0.88[CHB][hapmap]
rs1434235	0.84[CHD][hapmap]
rs17776569	0.94[CHB][hapmap]
rs1802539	0.88[CHB][hapmap]
rs1806299	0.93[YRI][hapmap]
rs1897787	0.88[CHB][hapmap]
rs1991928	0.88[CHB][hapmap]
rs2164061	0.84[CHD][hapmap]
rs2247355	0.87[CHB][hapmap]
rs2436844	0.84[CHD][hapmap]
rs2436849	0.88[CHB][hapmap]
rs2436856	0.88[CHB][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs2436861	0.81[CHB][hapmap]
rs2513912	0.88[CHB][hapmap];0.81[CHD][hapmap]
rs2513915	0.82[CHB][hapmap]
rs2513920	0.82[CHB][hapmap]
rs2513922	0.84[CHD][hapmap]
rs2513923	0.82[CHB][hapmap]
rs2570941	0.88[CHB][hapmap]
rs2679741	0.86[YRI][hapmap]
rs2679742	0.86[YRI][hapmap]
rs2679745	0.88[CHB][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap]
rs2679747	0.88[CHB][hapmap]
rs2679749	0.84[CHD][hapmap]
rs2679750	0.88[CHB][hapmap]
rs2679752	0.84[CHD][hapmap]
rs2679754	0.84[CHD][hapmap]
rs2679759	0.86[YRI][hapmap]
rs28594922	0.88[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2916559	0.88[CHB][hapmap]
rs3018954	0.82[CHB][hapmap]
rs529802	0.94[MEX][hapmap]
rs548488	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs567395	0.90[AFR][1000 genomes]
rs571241	0.87[MEX][hapmap]
rs581610	0.88[CHB][hapmap];0.87[MEX][hapmap]
rs601088	0.94[CHB][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap]
rs601588	0.86[YRI][hapmap]
rs665298	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs667927	0.93[YRI][hapmap]
rs678839	0.94[ASW][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs682651	0.81[MEX][hapmap]
rs7833202	0.83[YRI][hapmap]
rs892484	0.84[CHD][hapmap]
rs972142	0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1021898	chr8:103767324-103922482	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs565720	FZD6	cis	cerebellum	SCAN
rs565720	DCAF13	cis	parietal	SCAN
rs565720	AZIN1	cis	multi-tissue	Pritchard
rs565720	AZIN1	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103879200-103922000	Weak transcription	Fetal Intestine Small	intestine
2	chr8:103894200-103914600	Weak transcription	Fetal Lung	lung
3	chr8:103907400-103915000	Weak transcription	Fetal Stomach	stomach
4	chr8:103907600-103922600	Weak transcription	Brain Germinal Matrix	brain
5	chr8:103907800-103922000	Weak transcription	Fetal Brain Female	brain
6	chr8:103907800-103922600	Weak transcription	Gastric	stomach
7	chr8:103909200-103918200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:103909400-103918600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr8:103910200-103915000	Weak transcription	Pancreas	Pancrea
10	chr8:103910800-103915000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr8:103910800-103915400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr8:103910800-103921400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr8:103911000-103915000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr8:103911000-103915000	Weak transcription	Colon Smooth Muscle	Colon
15	chr8:103911000-103915400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr8:103911000-103919000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr8:103911000-103922000	Weak transcription	Aorta	Aorta
18	chr8:103911200-103915000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:103911200-103915000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr8:103911200-103915400	Weak transcription	Small Intestine	intestine
21	chr8:103911400-103914800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr8:103911400-103915000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr8:103911400-103915000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr8:103911400-103915000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr8:103911400-103915000	Weak transcription	HMEC	breast
26	chr8:103911400-103915600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr8:103911400-103915800	Weak transcription	HSMM	muscle
28	chr8:103911400-103918400	Weak transcription	Hela-S3	cervix
29	chr8:103911400-103922000	Weak transcription	Adipose Nuclei	Adipose
30	chr8:103911400-103922000	Weak transcription	Brain Substantia Nigra	brain
31	chr8:103911400-103922200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr8:103911400-103922200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr8:103911600-103915000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr8:103911600-103915400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr8:103911600-103915400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr8:103911600-103915600	Weak transcription	Brain Hippocampus Middle	brain
37	chr8:103911600-103921400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr8:103911800-103914400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr8:103911800-103914600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr8:103911800-103915000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr8:103911800-103915200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr8:103911800-103915200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr8:103911800-103921400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr8:103911800-103922600	Weak transcription	Left Ventricle	heart
45	chr8:103911800-103922600	Weak transcription	Lung	lung
46	chr8:103912000-103914600	Weak transcription	GM12878-XiMat	blood
47	chr8:103912000-103915400	Weak transcription	Primary T cells from cord blood	blood
48	chr8:103912400-103922600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr8:103913000-103915400	Weak transcription	HSMMtube	muscle
50	chr8:103913000-103915800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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