Variant report

Variant	rs17403175
Chromosome Location	chr11:10561957-10561958
allele	A/C
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	E2F4	chr11:10561458-10563005	MCF10A-Er-Src	breast:	n/a	chr11:10562533-10562542 chr11:10562787-10562796
2	POLR2A	chr11:10561314-10563085	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr11:10561915-10563093	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr11:10561917-10562055	HUVEC	blood vessel:	n/a	n/a
5	MAZ	chr11:10561553-10563196	IMR90	lung:	n/a	n/a
6	MYC	chr11:10561758-10562024	MCF10A-Er-Src	breast:	n/a	n/a
7	MXI1	chr11:10561562-10563951	IMR90	lung:	n/a	n/a
8	FOS	chr11:10561618-10562023	MCF10A-Er-Src	breast:	n/a	chr11:10561634-10561644 chr11:10561651-10561661 chr11:10561651-10561661
9	POLR2A	chr11:10561650-10562008	HCT-116	colon:	n/a	n/a
10	POLR2A	chr11:10561551-10563218	SK-N-MC	brain:	n/a	n/a
11	FOS	chr11:10561700-10562048	MCF10A-Er-Src	breast:	n/a	n/a
12	REST	chr11:10561831-10563363	H1-neurons	neurons:	n/a	chr11:10562649-10562669 chr11:10562648-10562657
13	MXI1	chr11:10561651-10564161	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr11:10561837-10563242	H1-neurons	neurons:	n/a	n/a
15	CEBPB	chr11:10561865-10561987	H1-hESC	embryonic stem cell:	n/a	n/a
16	MXI1	chr11:10561788-10563026	Hela-S3	cervix:	n/a	n/a
17	TBP	chr11:10561846-10562932	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr11:10561661-10563044	MCF10A-Er-Src	breast:	n/a	n/a
19	CTCF	chr11:10561826-10563494	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr11:10561872-10561972	ProgFib	skin:	n/a	n/a
21	CTCF	chr11:10561919-10563572	A549	lung:	n/a	n/a
22	MYC	chr11:10561700-10563434	MCF10A-Er-Src	breast:	n/a	n/a
23	HCFC1	chr11:10561249-10564110	Hela-S3	cervix:	n/a	n/a
24	MAX	chr11:10561953-10562397	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr11:10561942-10562377	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:10538298..10540845-chr11:10561134..10562717,2	MCF-7	breast:
2	chr11:10476884..10479039-chr11:10561132..10563728,3	K562	blood:
3	chr11:10519422..10522189-chr11:10559847..10562171,2	K562	blood:
4	chr11:10560102..10563921-chr11:10672313..10677222,4	MCF-7	breast:
5	chr11:10471184..10472852-chr11:10561290..10564176,2	K562	blood:

Variant related genes	Relation type
MRVI1-AS1	TF binding region
ENSG00000133805	Chromatin interaction
ENSG00000072952	Chromatin interaction
ENSG00000110315	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1346022	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1364738	1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364739	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1462940	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908001	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs16927077	1.00[CHD][hapmap]
rs17318955	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17403439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17403460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17403795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17403942	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17403977	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41464450	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4910160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910161	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6484336	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs7949992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952446	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv1044011	chr11:10529353-10564450	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17403175	OR10A5	cis	cerebellum	SCAN
rs17403175	SNORA45	cis	cerebellum	SCAN
rs17403175	MICAL2	cis	parietal	SCAN
rs17403175	AMPD3	cis	cerebellum	SCAN
rs17403175	C11orf17	cis	cerebellum	SCAN
rs17403175	RNF141	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10541600-10562000	Weak transcription	Gastric	stomach
2	chr11:10549400-10562000	Weak transcription	Spleen	Spleen
3	chr11:10560800-10562000	Flanking Active TSS	Osteobl	bone
4	chr11:10560800-10563200	Active TSS	Aorta	Aorta
5	chr11:10561200-10562200	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr11:10561200-10562200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:10561200-10562800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:10561200-10562800	Active TSS	HMEC	breast
9	chr11:10561200-10563400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:10561400-10562000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:10561400-10562000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:10561400-10562000	Flanking Active TSS	Brain Anterior Caudate	brain
13	chr11:10561400-10562000	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr11:10561400-10562000	Flanking Active TSS	Fetal Brain Male	brain
15	chr11:10561400-10562000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr11:10561400-10562000	Flanking Active TSS	NH-A	brain
17	chr11:10561400-10562200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr11:10561400-10562200	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr11:10561400-10562200	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr11:10561400-10562200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr11:10561400-10562200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:10561400-10562200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:10561400-10562200	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr11:10561400-10562200	Flanking Active TSS	Fetal Lung	lung
25	chr11:10561400-10562200	Flanking Active TSS	Dnd41	blood
26	chr11:10561400-10562200	Flanking Active TSS	HUVEC	blood vessel
27	chr11:10561400-10562400	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr11:10561400-10563000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:10561400-10563200	Active TSS	Right Atrium	heart
30	chr11:10561400-10563200	Active TSS	NHDF-Ad	bronchial
31	chr11:10561400-10563400	Active TSS	Stomach Smooth Muscle	stomach
32	chr11:10561400-10563400	Active TSS	NHLF	lung
33	chr11:10561600-10562000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr11:10561600-10562000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr11:10561600-10562000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
36	chr11:10561600-10562000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
37	chr11:10561600-10562000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
38	chr11:10561600-10562000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:10561600-10562000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:10561600-10562000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr11:10561600-10562000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr11:10561600-10562000	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr11:10561600-10562000	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr11:10561600-10562000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr11:10561600-10562000	Flanking Active TSS	Fetal Brain Female	brain
46	chr11:10561600-10562000	Flanking Active TSS	Fetal Intestine Large	intestine
47	chr11:10561600-10562000	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr11:10561600-10562000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr11:10561600-10562000	Flanking Active TSS	Stomach Mucosa	stomach
50	chr11:10561600-10562000	Flanking Active TSS	Thymus	Thymus

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