Variant report

Variant	rs601088
Chromosome Location	chr8:103914604-103914605
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: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10104995	0.88[AFR][1000 genomes]
rs1019976	0.94[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1062048	0.94[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11776547	0.90[AFR][1000 genomes]
rs11993347	0.90[AFR][1000 genomes]
rs1434235	0.91[YRI][hapmap]
rs17776569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17776600	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1802539	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1806300	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1897787	0.94[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1982111	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1991928	0.94[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2164061	0.91[YRI][hapmap]
rs2247355	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2256440	0.91[YRI][hapmap]
rs2436844	0.84[YRI][hapmap]
rs2436849	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2436851	0.81[ASN][1000 genomes]
rs2436856	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2436861	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2513876	0.91[ASN][1000 genomes]
rs2513877	0.96[EUR][1000 genomes]
rs2513911	0.81[CHB][hapmap];0.83[GIH][hapmap]
rs2513912	0.94[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2513915	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2513917	0.81[ASN][1000 genomes]
rs2513919	0.91[YRI][hapmap]
rs2513920	0.87[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2513921	0.84[YRI][hapmap]
rs2513923	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2513936	0.83[ASN][1000 genomes]
rs2570941	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2570942	0.91[YRI][hapmap]
rs2570945	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2570951	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2570952	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2679736	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2679737	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2679740	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2679745	0.93[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2679747	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2679749	0.91[YRI][hapmap]
rs2679750	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2679753	0.91[ASN][1000 genomes]
rs2679754	0.91[YRI][hapmap]
rs2679756	0.91[YRI][hapmap]
rs2679757	0.91[YRI][hapmap]
rs2916559	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3018943	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3018954	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs34157576	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35656046	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529802	0.93[MEX][hapmap]
rs565720	0.94[CHB][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap]
rs571241	0.87[MEX][hapmap]
rs581610	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs677406	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs682651	0.81[MEX][hapmap]
rs688791	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs972142	0.91[YRI][hapmap]
rs974758	0.83[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs601088	DCAF13	cis	parietal	SCAN
rs601088	AZIN1	cis	parietal	SCAN
rs601088	AZIN1	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 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	chr8:103907400-103915000	Weak transcription	Fetal Stomach	stomach
3	chr8:103907600-103922600	Weak transcription	Brain Germinal Matrix	brain
4	chr8:103907800-103922000	Weak transcription	Fetal Brain Female	brain
5	chr8:103907800-103922600	Weak transcription	Gastric	stomach
6	chr8:103909200-103918200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:103909400-103918600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr8:103910200-103915000	Weak transcription	Pancreas	Pancrea
9	chr8:103910800-103915000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr8:103910800-103915400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr8:103910800-103921400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr8:103911000-103915000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr8:103911000-103915000	Weak transcription	Colon Smooth Muscle	Colon
14	chr8:103911000-103915400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr8:103911000-103919000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr8:103911000-103922000	Weak transcription	Aorta	Aorta
17	chr8:103911200-103915000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr8:103911200-103915000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr8:103911200-103915400	Weak transcription	Small Intestine	intestine
20	chr8:103911400-103914800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr8:103911400-103915000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr8:103911400-103915000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr8:103911400-103915000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr8:103911400-103915000	Weak transcription	HMEC	breast
25	chr8:103911400-103915600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr8:103911400-103915800	Weak transcription	HSMM	muscle
27	chr8:103911400-103918400	Weak transcription	Hela-S3	cervix
28	chr8:103911400-103922000	Weak transcription	Adipose Nuclei	Adipose
29	chr8:103911400-103922000	Weak transcription	Brain Substantia Nigra	brain
30	chr8:103911400-103922200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr8:103911400-103922200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr8:103911600-103915000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr8:103911600-103915400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr8:103911600-103915400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr8:103911600-103915600	Weak transcription	Brain Hippocampus Middle	brain
36	chr8:103911600-103921400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr8:103911800-103915000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr8:103911800-103915200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr8:103911800-103915200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr8:103911800-103921400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr8:103911800-103922600	Weak transcription	Left Ventricle	heart
42	chr8:103911800-103922600	Weak transcription	Lung	lung
43	chr8:103912000-103915400	Weak transcription	Primary T cells from cord blood	blood
44	chr8:103912400-103922600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr8:103913000-103915400	Weak transcription	HSMMtube	muscle
46	chr8:103913000-103915800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr8:103913000-103916600	Weak transcription	Fetal Muscle Leg	muscle
48	chr8:103913200-103915000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr8:103913200-103915000	Weak transcription	Right Atrium	heart
50	chr8:103913400-103915000	Weak transcription	Placenta	Placenta

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