Variant report

Variant	rs2041393
Chromosome Location	chr17:17206349-17206350
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:111)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:111 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr17:17206306-17207153	K562	blood:	n/a	n/a
2	ZMIZ1	chr17:17206321-17206785	K562	blood:	n/a	n/a
3	TCF12	chr17:17206232-17206949	A549	lung:	n/a	n/a
4	WRNIP1	chr17:17206325-17206506	GM12878	blood:	n/a	n/a
5	POLR2A	chr17:17206251-17207008	HL-60	blood:	n/a	n/a
6	MAX	chr17:17206335-17207409	HepG2	liver:	n/a	n/a
7	MXI1	chr17:17205972-17209515	SK-N-SH	brain:	n/a	chr17:17208730-17208739
8	POLR2A	chr17:17206348-17207320	GM19193	blood:	n/a	n/a
9	ATF2	chr17:17206190-17206483	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr17:17206250-17207297	NB4	blood:	n/a	n/a
11	POLR2A	chr17:17206156-17206855	U87	brain:	n/a	n/a
12	MAX	chr17:17206306-17207373	HepG2	liver:	n/a	n/a
13	MYC	chr17:17206341-17206405	K562	blood:	n/a	n/a
14	MAX	chr17:17206329-17207345	MCF-7	breast:	n/a	n/a
15	E2F4	chr17:17206190-17207306	MCF10A-Er-Src	breast:	n/a	n/a
16	MYC	chr17:17206284-17206758	MCF10A-Er-Src	breast:	n/a	n/a
17	TAF1	chr17:17206305-17206879	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr17:17206202-17207329	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr17:17206312-17207232	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr17:17206284-17206845	SK-N-MC	brain:	n/a	n/a
21	E2F6	chr17:17206225-17207492	A549	lung:	n/a	chr17:17206952-17206963
22	HA-E2F1	chr17:17206340-17207211	Hela-S3	cervix:	n/a	chr17:17206562-17206573
23	YY1	chr17:17206341-17206625	GM12878	blood:	n/a	n/a
24	POLR2A	chr17:17206337-17206929	H1-hESC	embryonic stem cell:	n/a	n/a
25	ARID3A	chr17:17206250-17206725	K562	blood:	n/a	n/a
26	HEY1	chr17:17206252-17207241	K562	blood:	n/a	n/a
27	POLR2A	chr17:17206251-17207180	MCF10A-Er-Src	breast:	n/a	n/a
28	BACH1	chr17:17206349-17206948	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr17:17206263-17207234	GM12878	blood:	n/a	n/a
30	REST	chr17:17206104-17206944	H1-neurons	neurons:	n/a	n/a
31	MAX	chr17:17206242-17207427	HCT-116	colon:	n/a	n/a
32	POLR2A	chr17:17206318-17206876	GM12891	blood:	n/a	n/a
33	HEY1	chr17:17206345-17206927	HepG2	liver:	n/a	n/a
34	CUX1	chr17:17206303-17206577	K562	blood:	n/a	n/a
35	CREB1	chr17:17206281-17207230	HepG2	liver:	n/a	n/a
36	MYC	chr17:17206311-17208259	K562	blood:	n/a	n/a
37	MAX	chr17:17206270-17207317	ECC-1	luminal epithelium:	n/a	n/a
38	REST	chr17:17206179-17206743	A549	lung:	n/a	n/a
39	POLR2A	chr17:17206325-17207241	MCF-7	breast:	n/a	n/a
40	POLR2A	chr17:17206234-17206884	HCT-116	colon:	n/a	n/a
41	POLR2A	chr17:17206299-17209208	K562	blood:	n/a	n/a
42	POLR2A	chr17:17206201-17207156	PBDE	blood:	n/a	n/a
43	RCOR1	chr17:17206341-17206690	K562	blood:	n/a	n/a
44	RCOR1	chr17:17206259-17209023	K562	blood:	n/a	n/a
45	MTA3	chr17:17206232-17206630	GM12878	blood:	n/a	n/a
46	POLR2A	chr17:17206224-17206922	PFSK-1	brain:	n/a	n/a
47	CBX3	chr17:17206257-17206681	K562	blood:	n/a	n/a
48	POLR2A	chr17:17206280-17207365	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr17:17206322-17207384	K562	blood:	n/a	n/a
50	E2F6	chr17:17206310-17207304	H1-hESC	embryonic stem cell:	n/a	chr17:17206952-17206963

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:17088943..17091453-chr17:17205581..17207911,3	K562	blood:
2	chr17:17183059..17186537-chr17:17204352..17209458,5	K562	blood:
3	chr17:17182421..17186483-chr17:17204152..17209830,5	MCF-7	breast:
4	chr17:17137888..17140600-chr17:17205281..17208205,3	MCF-7	breast:
5	chr17:17109423..17111075-chr17:17206335..17209184,2	K562	blood:
6	chr17:17138742..17142464-chr17:17205516..17208012,3	MCF-7	breast:
7	chr17:17183415..17186229-chr17:17206165..17209020,3	MCF-7	breast:
8	chr17:17181690..17186423-chr17:17204352..17210529,13	K562	blood:

No data

Variant related genes	Relation type
NT5M	TF binding region
ENSG00000133030	Chromatin interaction
ENSG00000266498	Chromatin interaction
ENSG00000264187	Chromatin interaction
ENSG00000141030	Chromatin interaction
ENSG00000154803	Chromatin interaction
ENSG00000179598	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12451886	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12950929	0.84[AMR][1000 genomes]
rs62066114	0.92[ASN][1000 genomes]
rs62066115	0.95[ASN][1000 genomes]
rs6502577	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6502578	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7207856	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7217114	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7217162	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9889367	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9889738	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9895057	0.97[ASN][1000 genomes]
rs9896977	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9899615	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9907711	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9907857	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9908360	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9908807	0.97[ASN][1000 genomes]
rs9909111	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9909850	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9912109	1.00[CEU][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065811	chr17:17104760-17225204	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv833382	chr17:17124329-17305683	Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv469777	chr17:17127385-17272698	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv482546	chr17:17127385-17272698	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv33859	chr17:17189904-17208157	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv1061186	chr17:17200427-17314406	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	esv3408202	chr17:17205752-17208600	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	esv3351525	chr17:17205977-17207925	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2041393	COPS3	cis	multi-tissue	Pritchard
rs2041393	FLII	cis	parietal	SCAN
rs2041393	FLCN	cis	lymphoblastoid	seeQTL
rs2041393	TNFRSF13B	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17202000-17206400	Weak transcription	HSMM	muscle
2	chr17:17203400-17207000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr17:17203600-17207000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr17:17204600-17206400	Weak transcription	Aorta	Aorta
5	chr17:17204600-17206400	Weak transcription	Esophagus	oesophagus
6	chr17:17204600-17206400	Weak transcription	Gastric	stomach
7	chr17:17204600-17206400	Weak transcription	Pancreas	Pancrea
8	chr17:17204600-17206400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:17204800-17206400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:17205000-17206400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr17:17205200-17206400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:17205600-17206600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr17:17205600-17206600	Flanking Active TSS	Dnd41	blood
14	chr17:17205800-17206600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:17205800-17207400	Active TSS	Hela-S3	cervix
16	chr17:17205800-17207600	Active TSS	K562	blood
17	chr17:17206000-17206400	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr17:17206000-17206400	Enhancers	Colonic Mucosa	Colon
19	chr17:17206000-17206400	Flanking Active TSS	HepG2	liver
20	chr17:17206000-17206600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr17:17206000-17207200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr17:17206000-17207200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:17206000-17207200	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr17:17206000-17207200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr17:17206000-17207200	Active TSS	Brain Germinal Matrix	brain
26	chr17:17206000-17207200	Active TSS	Osteobl	bone
27	chr17:17206000-17207400	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr17:17206000-17207400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr17:17206000-17207400	Active TSS	Brain Cingulate Gyrus	brain
30	chr17:17206000-17207400	Active TSS	Fetal Stomach	stomach
31	chr17:17206000-17207400	Active TSS	A549	lung
32	chr17:17206000-17207600	Active TSS	Fetal Lung	lung
33	chr17:17206000-17208600	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr17:17206200-17206400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
35	chr17:17206200-17206400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr17:17206200-17206400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr17:17206200-17206400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr17:17206200-17206400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr17:17206200-17206400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr17:17206200-17206400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr17:17206200-17206400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr17:17206200-17206400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr17:17206200-17206400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr17:17206200-17206400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr17:17206200-17206400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr17:17206200-17206400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr17:17206200-17206400	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr17:17206200-17206400	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr17:17206200-17206400	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr17:17206200-17206400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland

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