Variant report

Variant	rs2001381
Chromosome Location	chr17:45940302-45940303
allele	C/T
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	MAX	chr17:45940084-45940931	A549	lung:	n/a	n/a
2	PBX3	chr17:45940115-45940842	SK-N-SH	brain:	n/a	n/a
3	USF1	chr17:45940285-45940955	A549	lung:	n/a	n/a
4	FOSL1	chr17:45940153-45940958	HCT-116	colon:	n/a	n/a
5	JUND	chr17:45940100-45940997	HCT-116	colon:	n/a	n/a
6	FOSL2	chr17:45940068-45941014	A549	lung:	n/a	n/a
7	SPI1	chr17:45940250-45940392	K562	blood:	n/a	chr17:45940341-45940350 chr17:45940339-45940352 chr17:45940338-45940351
8	PBX3	chr17:45940258-45940913	SK-N-SH	brain:	n/a	n/a
9	ELF1	chr17:45940287-45940503	K562	blood:	n/a	chr17:45940340-45940351
10	FOSL2	chr17:45940273-45940832	A549	lung:	n/a	n/a
11	ELF1	chr17:45939970-45940577	K562	blood:	n/a	chr17:45940340-45940351 chr17:45940126-45940137
12	GATA3	chr17:45940023-45941044	A549	lung:	n/a	chr17:45940495-45940505
13	FOSL1	chr17:45939872-45940933	HCT-116	colon:	n/a	n/a
14	JUND	chr17:45940160-45940986	HCT-116	colon:	n/a	n/a
15	SMC3	chr17:45940279-45940715	Hela-S3	cervix:	n/a	n/a
16	MAX	chr17:45940009-45941012	HCT-116	colon:	n/a	n/a
17	SP1	chr17:45939886-45940944	HCT-116	colon:	n/a	n/a
18	RCOR1	chr17:45939897-45940986	IMR90	lung:	n/a	n/a
19	SP1	chr17:45940153-45940944	A549	lung:	n/a	n/a
20	SP1	chr17:45939991-45940919	HCT-116	colon:	n/a	n/a
21	SPI1	chr17:45940201-45940430	GM12891	blood:	n/a	chr17:45940341-45940350 chr17:45940339-45940352 chr17:45940338-45940351
22	E2F6	chr17:45940272-45940882	A549	lung:	n/a	n/a
23	CBX3	chr17:45940147-45940975	HCT-116	colon:	n/a	n/a
24	EP300	chr17:45940243-45940897	A549	lung:	n/a	chr17:45940341-45940350
25	ELF1	chr17:45940158-45940779	A549	lung:	n/a	chr17:45940340-45940351
26	GABPA	chr17:45940205-45940787	A549	lung:	n/a	n/a
27	SPI1	chr17:45940083-45940600	HL-60	blood:	n/a	chr17:45940341-45940350 chr17:45940126-45940135 chr17:45940339-45940352 chr17:45940338-45940351
28	JUN	chr17:45940235-45940937	K562	blood:	n/a	n/a
29	MYC	chr17:45939921-45940973	A549	lung:	n/a	chr17:45939973-45939982
30	MAX	chr17:45939875-45940931	A549	lung:	n/a	chr17:45939973-45939982
31	MAX	chr17:45940019-45940994	HCT-116	colon:	n/a	n/a
32	TCF12	chr17:45939906-45941000	A549	lung:	n/a	chr17:45940456-45940463 chr17:45940457-45940467
33	ELF1	chr17:45939999-45940654	A549	lung:	n/a	chr17:45940340-45940351 chr17:45940126-45940137
34	HNF4A	chr17:45940060-45940320	HepG2	liver:	n/a	chr17:45940179-45940194 chr17:45940179-45940194
35	ELF1	chr17:45940145-45940469	GM12878	blood:	n/a	chr17:45940340-45940351
36	EP300	chr17:45940005-45940991	A549	lung:	n/a	chr17:45940341-45940350 chr17:45940126-45940135
37	MAX	chr17:45940048-45940825	Hela-S3	cervix:	n/a	n/a
38	SMARCC1	chr17:45940077-45940783	Hela-S3	cervix:	n/a	n/a
39	MAX	chr17:45940249-45940927	SK-N-SH	brain:	n/a	n/a
40	CBX3	chr17:45939914-45941013	HCT-116	colon:	n/a	n/a
41	FOSL2	chr17:45940195-45940943	SK-N-SH	brain:	n/a	n/a
42	SP1	chr17:45940212-45940958	A549	lung:	n/a	n/a
43	JUND	chr17:45940227-45940958	SK-N-SH	brain:	n/a	n/a
44	SPI1	chr17:45940188-45940415	GM12878	blood:	n/a	chr17:45940341-45940350 chr17:45940339-45940352 chr17:45940338-45940351

No.	Distal block	Cell Line	Cell type
1	chr17:45939167..45942098-chr17:45971547..45974421,3	MCF-7	breast:
2	chr17:45924111..45929589-chr17:45940263..45947435,9	MCF-7	breast:
3	chr17:45940066..45942242-chr17:45971529..45973445,2	K562	blood:

Variant related genes	Relation type
ENSG00000264243	TF binding region
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000189120	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1005655	0.81[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs11079796	0.81[MEX][hapmap];0.86[TSI][hapmap]
rs11650536	0.81[MEX][hapmap];0.86[TSI][hapmap]
rs16948722	0.82[EUR][1000 genomes]
rs2001380	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3803856	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3809869	0.81[MEX][hapmap];0.86[TSI][hapmap]
rs4362431	0.85[CHB][hapmap]
rs4794203	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs701984	0.81[MEX][hapmap];0.86[TSI][hapmap]
rs8064241	0.90[CHB][hapmap]
rs8075360	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9904820	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2001381	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs2001381	SNX11	cis	cerebellum	SCAN
rs2001381	SNX11	cis	parietal	SCAN
rs2001381	VAT1	cis	cerebellum	SCAN
rs2001381	SCRN2	cis	Whole Blood	GTEx
rs2001381	OSBPL7	cis	Thyroid	GTEx
rs2001381	DUSP3	cis	parietal	SCAN
rs2001381	RPL27	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45935800-45942200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:45935800-45946400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:45937600-45940400	Weak transcription	K562	blood
4	chr17:45939600-45945400	Enhancers	Placenta	Placenta
5	chr17:45939800-45940800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr17:45939800-45940800	Enhancers	HepG2	liver
7	chr17:45939800-45942000	Enhancers	HMEC	breast
8	chr17:45939800-45942000	Enhancers	NHEK	skin
9	chr17:45940000-45940400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr17:45940000-45940400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr17:45940000-45940400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr17:45940000-45940400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr17:45940000-45940400	Flanking Active TSS	HSMMtube	muscle
14	chr17:45940000-45940600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr17:45940000-45940600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr17:45940000-45940600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:45940000-45940600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:45940000-45940600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr17:45940000-45940600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr17:45940000-45940600	Enhancers	Duodenum Mucosa	Duodenum
21	chr17:45940000-45940600	Enhancers	Fetal Lung	lung
22	chr17:45940000-45940600	Enhancers	Fetal Thymus	thymus
23	chr17:45940000-45940600	Enhancers	Lung	lung
24	chr17:45940000-45940600	Flanking Active TSS	Osteobl	bone
25	chr17:45940000-45940800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr17:45940000-45940800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:45940000-45940800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:45940000-45940800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr17:45940000-45940800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr17:45940000-45940800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr17:45940000-45940800	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr17:45940000-45940800	Enhancers	Spleen	Spleen
33	chr17:45940000-45940800	Flanking Active TSS	A549	lung
34	chr17:45940000-45940800	Flanking Active TSS	Hela-S3	cervix
35	chr17:45940000-45940800	Enhancers	HUVEC	blood vessel
36	chr17:45940000-45940800	Enhancers	NH-A	brain
37	chr17:45940000-45940800	Enhancers	NHLF	lung
38	chr17:45940000-45941200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr17:45940000-45941200	Enhancers	NHDF-Ad	bronchial
40	chr17:45940000-45942000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr17:45940000-45942000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr17:45940000-45943200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr17:45940200-45940400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr17:45940200-45940400	Flanking Active TSS	HSMM	muscle
45	chr17:45940200-45940600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr17:45940200-45940600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr17:45940200-45940600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr17:45940200-45940600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr17:45940200-45940800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr17:45940200-45940800	Enhancers	Primary T cells from cord blood	blood

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