Variant report

Variant	rs667927
Chromosome Location	chr8:103912414-103912415
allele	A/T
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	chr8:103878683..103881066-chr8:103911212..103913348,2	MCF-7	breast:
3	chr8:103909625..103914681-chr8:103915019..103918768,8	MCF-7	breast:
4	chr8:103911797..103913413-chr8:103915320..103917668,2	K562	blood:
5	chr8:103903395..103905435-chr8:103912385..103915123,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253320	Chromatin interaction
ENSG00000253263	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10104704	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1055376	0.83[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10808382	1.00[JPT][hapmap]
rs1138	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1714399	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1806299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961102	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1991927	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2117313	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2304346	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2436857	1.00[JPT][hapmap]
rs2513910	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs2513922	0.82[ASW][hapmap]
rs2513935	0.83[YRI][hapmap]
rs2570939	0.88[ASN][1000 genomes]
rs2570940	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2570944	0.97[ASN][1000 genomes]
rs2570946	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2570947	0.97[EUR][1000 genomes]
rs2570948	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570949	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2570950	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2679741	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2679742	0.96[CEU][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2679744	0.97[ASN][1000 genomes]
rs2679746	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2679748	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2679752	0.88[ASW][hapmap];0.91[LWK][hapmap];0.80[YRI][hapmap]
rs2679758	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2679759	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28594922	0.85[AFR][1000 genomes]
rs2916558	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2916560	0.97[ASN][1000 genomes]
rs2916561	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs491770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs522547	0.86[ASN][1000 genomes]
rs548488	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs551241	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565720	0.93[YRI][hapmap]
rs567395	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs587946	0.86[CHD][hapmap]
rs599777	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs601588	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606335	0.99[ASN][1000 genomes]
rs608236	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs613049	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs613559	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs644299	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs647313	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657000	0.86[ASN][1000 genomes]
rs665298	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs678839	0.83[GIH][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs6921	0.83[ASN][1000 genomes]
rs7833202	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs892485	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs892486	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[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
rs667927	BAALC	cis	parietal	SCAN
rs667927	AZIN1	cis	multi-tissue	Pritchard
rs667927	AZIN1	cis	parietal	SCAN

Chromatin state (count:70 , 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	chr8:103907200-103912800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr8:103907400-103915000	Weak transcription	Fetal Stomach	stomach
5	chr8:103907600-103922600	Weak transcription	Brain Germinal Matrix	brain
6	chr8:103907800-103922000	Weak transcription	Fetal Brain Female	brain
7	chr8:103907800-103922600	Weak transcription	Gastric	stomach
8	chr8:103908000-103913200	Weak transcription	Spleen	Spleen
9	chr8:103908800-103913000	Enhancers	Fetal Muscle Leg	muscle
10	chr8:103909000-103913400	Enhancers	Psoas Muscle	Psoas
11	chr8:103909200-103918200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:103909400-103918600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr8:103910000-103913000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr8:103910000-103914200	Enhancers	Fetal Thymus	thymus
15	chr8:103910200-103913400	Enhancers	Thymus	Thymus
16	chr8:103910200-103915000	Weak transcription	Pancreas	Pancrea
17	chr8:103910800-103915000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr8:103910800-103915400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr8:103910800-103921400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr8:103911000-103913400	Enhancers	Primary hematopoietic stem cells	blood
21	chr8:103911000-103915000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr8:103911000-103915000	Weak transcription	Colon Smooth Muscle	Colon
23	chr8:103911000-103915400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr8:103911000-103919000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr8:103911000-103922000	Weak transcription	Aorta	Aorta
26	chr8:103911200-103913400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr8:103911200-103913800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr8:103911200-103914200	Weak transcription	Liver	Liver
29	chr8:103911200-103915000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr8:103911200-103915000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr8:103911200-103915400	Weak transcription	Small Intestine	intestine
32	chr8:103911400-103912800	Weak transcription	Right Ventricle	heart
33	chr8:103911400-103912800	Enhancers	Dnd41	blood
34	chr8:103911400-103913400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr8:103911400-103914800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr8:103911400-103915000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr8:103911400-103915000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr8:103911400-103915000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr8:103911400-103915000	Weak transcription	HMEC	breast
40	chr8:103911400-103915600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr8:103911400-103915800	Weak transcription	HSMM	muscle
42	chr8:103911400-103918400	Weak transcription	Hela-S3	cervix
43	chr8:103911400-103922000	Weak transcription	Adipose Nuclei	Adipose
44	chr8:103911400-103922000	Weak transcription	Brain Substantia Nigra	brain
45	chr8:103911400-103922200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr8:103911400-103922200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr8:103911600-103913400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr8:103911600-103913400	Enhancers	Placenta	Placenta
49	chr8:103911600-103915000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr8:103911600-103915400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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