Variant report

Variant	rs1986693
Chromosome Location	chr17:46026156-46026157
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:108)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:108 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr17:46025906-46026551	HepG2	liver:	n/a	n/a
2	POLR2A	chr17:46025993-46026569	A549	lung:	n/a	n/a
3	CEBPB	chr17:46026105-46027045	HepG2	liver:	n/a	n/a
4	MAX	chr17:46025809-46027314	A549	lung:	n/a	n/a
5	CTCF	chr17:46026037-46027397	HCT-116	colon:	n/a	chr17:46026781-46026802 chr17:46026782-46026795 chr17:46026780-46026796 chr17:46026779-46026797
6	POLR2A	chr17:46025886-46028079	HepG2	liver:	n/a	n/a
7	MYBL2	chr17:46025812-46027164	HepG2	liver:	n/a	n/a
8	USF2	chr17:46026054-46026208	HepG2	liver:	n/a	n/a
9	SP1	chr17:46025857-46027042	A549	lung:	n/a	n/a
10	GATA3	chr17:46025977-46026473	T-47D	breast:	n/a	n/a
11	FOXA1	chr17:46025879-46026518	HepG2	liver:	n/a	n/a
12	SP1	chr17:46025841-46027130	A549	lung:	n/a	n/a
13	CEBPB	chr17:46025949-46027055	A549	lung:	n/a	n/a
14	FOS	chr17:46026140-46026315	MCF10A-Er-Src	breast:	n/a	n/a
15	FOXA1	chr17:46025940-46026582	HepG2	liver:	n/a	n/a
16	POLR2A	chr17:46025340-46027191	MCF10A-Er-Src	breast:	n/a	n/a
17	EP300	chr17:46025765-46026806	A549	lung:	n/a	n/a
18	SMC3	chr17:46026088-46027072	HepG2	liver:	n/a	chr17:46026781-46026795
19	YY1	chr17:46026023-46027060	HepG2	liver:	n/a	chr17:46026794-46026803
20	MAFK	chr17:46026106-46026437	HepG2	liver:	n/a	n/a
21	HDAC2	chr17:46025974-46027047	HepG2	liver:	n/a	n/a
22	FOXA2	chr17:46025817-46027073	A549	lung:	n/a	n/a
23	FOSL2	chr17:46025855-46026560	HepG2	liver:	n/a	n/a
24	TCF7L2	chr17:46026079-46026309	PANC-1	pancreas:	n/a	n/a
25	RAD21	chr17:46026024-46027275	HCT-116	colon:	n/a	chr17:46026780-46026799
26	CTCF	chr17:46026100-46026250	RPTEC	kidney:	n/a	n/a
27	EP300	chr17:46025836-46027220	A549	lung:	n/a	n/a
28	NR3C1	chr17:46025937-46026649	A549	lung:	n/a	n/a
29	CTCF	chr17:46026020-46026170	HPAF	blood vessel:	n/a	n/a
30	MYBL2	chr17:46025807-46027244	HepG2	liver:	n/a	n/a
31	MBD4	chr17:46025954-46027033	HepG2	liver:	n/a	n/a
32	FOSL2	chr17:46025989-46026902	A549	lung:	n/a	n/a
33	RAD21	chr17:46026006-46027255	A549	lung:	n/a	chr17:46026780-46026799
34	POLR2A	chr17:46026004-46026519	HepG2	liver:	n/a	n/a
35	NR3C1	chr17:46026023-46026586	A549	lung:	n/a	n/a
36	POLR2A	chr17:46026119-46026163	ProgFib	skin:	n/a	n/a
37	ELF1	chr17:46025871-46027669	MCF-7	breast:	n/a	chr17:46027412-46027423
38	MAX	chr17:46025916-46027747	MCF-7	breast:	n/a	n/a
39	FOXA1	chr17:46025976-46026506	T-47D	breast:	n/a	n/a
40	BCL3	chr17:46025893-46027407	A549	lung:	n/a	n/a
41	CTCF	chr17:46026140-46026290	GM12868	blood:	n/a	n/a
42	SP1	chr17:46025942-46026590	HepG2	liver:	n/a	n/a
43	BCL3	chr17:46025853-46027404	A549	lung:	n/a	n/a
44	NR3C1	chr17:46025938-46026835	A549	lung:	n/a	n/a
45	MYC	chr17:46026083-46026317	HepG2	liver:	n/a	n/a
46	POLR2A	chr17:46025953-46027582	Hela-S3	cervix:	n/a	n/a
47	FOXA2	chr17:46025914-46026977	A549	lung:	n/a	n/a
48	CTCF	chr17:46026140-46026290	HAc	cerebellar:	n/a	n/a
49	JUND	chr17:46026030-46026467	HepG2	liver:	n/a	n/a
50	CTCF	chr17:46026060-46026210	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:45920268..45920780-chr17:46025947..46026606,2	MCF-7	breast:
2	chr17:45970281..45975378-chr17:46022719..46027732,11	MCF-7	breast:
3	chr17:46026023..46027620-chr17:46047369..46048630,14	MCF-7	breast:
4	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
5	chr17:46008254..46011151-chr17:46023044..46026189,3	MCF-7	breast:
6	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
7	chr17:46024543..46026331-chr17:46053891..46056374,2	K562	blood:
8	chr17:46026020..46027520-chr17:46047710..46048729,27	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000264019	TF binding region
ENSG00000266601	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12951323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16952265	0.82[CEU][hapmap]
rs41336845	0.88[CEU][hapmap];0.92[TSI][hapmap]
rs4794321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823509	0.92[EUR][1000 genomes]
rs72823513	0.92[EUR][1000 genomes]
rs8073371	0.88[CEU][hapmap];0.96[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1986693	PNPO	cis	parietal	SCAN
rs1986693	CDK5RAP3	cis	parietal	SCAN
rs1986693	TTC25	cis	parietal	SCAN
rs1986693	LEPREL4	cis	cerebellum	SCAN
rs1986693	KRT17	cis	cerebellum	SCAN
rs1986693	NPEPPS	cis	cerebellum	SCAN
rs1986693	PNPO	cis	cerebellum	SCAN
rs1986693	TUBG1	cis	parietal	SCAN
rs1986693	AOC3	cis	parietal	SCAN
rs1986693	CDK5RAP3	cis	cerebellum	SCAN
rs1986693	RPL27	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019600-46027000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:46019800-46026800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:46019800-46026800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr17:46019800-46026800	Weak transcription	Brain Germinal Matrix	brain
5	chr17:46019800-46026800	Weak transcription	HSMMtube	muscle
6	chr17:46019800-46027400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
9	chr17:46020000-46026200	Weak transcription	Fetal Kidney	kidney
10	chr17:46020000-46026400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr17:46020000-46026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr17:46020000-46026400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr17:46020000-46026800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr17:46020000-46026800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr17:46020000-46027000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr17:46020000-46034600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr17:46020200-46026200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr17:46020200-46026200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr17:46020200-46026800	Weak transcription	HUVEC	blood vessel
20	chr17:46021600-46026200	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr17:46022800-46026200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr17:46022800-46026400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr17:46023000-46026200	Weak transcription	NH-A	brain
24	chr17:46023000-46026400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr17:46023000-46026600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr17:46023000-46026800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr17:46023200-46026600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr17:46023200-46026600	Weak transcription	Fetal Brain Female	brain
29	chr17:46023200-46026800	Genic enhancers	Fetal Intestine Small	intestine
30	chr17:46023200-46030000	Genic enhancers	Fetal Intestine Large	intestine
31	chr17:46023600-46026200	Weak transcription	Left Ventricle	heart
32	chr17:46023600-46026800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr17:46023800-46026200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr17:46024000-46026200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr17:46024000-46026200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr17:46024000-46026400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:46024000-46026400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr17:46024000-46027000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr17:46024200-46026200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr17:46024200-46026200	Weak transcription	Right Atrium	heart
41	chr17:46024200-46026400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr17:46024200-46026400	Enhancers	Liver	Liver
43	chr17:46024200-46026400	Weak transcription	Spleen	Spleen
44	chr17:46024200-46026800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr17:46024200-46027200	Weak transcription	Right Ventricle	heart
46	chr17:46024400-46026200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr17:46024400-46026400	Weak transcription	Brain Angular Gyrus	brain
48	chr17:46024400-46026400	Weak transcription	Thymus	Thymus
49	chr17:46024400-46031600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr17:46024600-46026200	Weak transcription	Fetal Muscle Trunk	muscle

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