Variant report

Variant	rs17617010
Chromosome Location	chr17:46049533-46049534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr17:46047522-46050410	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr17:46049424-46050825	K562	blood:	n/a	n/a
3	MXI1	chr17:46047255-46050557	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr17:46049516-46049780	MCF10A-Er-Src	breast:	n/a	n/a
5	MXI1	chr17:46047494-46049540	IMR90	lung:	n/a	n/a
6	NR2F2	chr17:46047840-46049590	K562	blood:	n/a	n/a
7	CTCF	chr17:46047393-46050115	A549	lung:	n/a	chr17:46048168-46048177
8	POLR2A	chr17:46047811-46049607	HepG2	liver:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45916805..45918645-chr17:46049307..46052220,2	MCF-7	breast:
2	chr17:46047400..46050259-chr17:46124707..46126731,3	MCF-7	breast:
3	chr17:45932084..45934510-chr17:46047359..46049635,2	K562	blood:
4	chr17:45915738..45918906-chr17:46047433..46049662,3	K562	blood:
5	chr17:46048621..46050545-chr17:46057076..46059668,3	K562	blood:
6	chr17:46033549..46039001-chr17:46046732..46050276,6	K562	blood:
7	chr17:46017765..46021634-chr17:46045854..46051133,6	MCF-7	breast:
8	chr17:45971266..45974117-chr17:46049059..46051074,2	MCF-7	breast:
9	chr17:45971215..45974947-chr17:46046480..46050487,6	MCF-7	breast:
10	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
11	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
12	chr17:45727256..45728937-chr17:46047807..46049675,2	K562	blood:
13	chr17:46048432..46050374-chr17:46050535..46053358,3	MCF-7	breast:
14	chr17:46048551..46050173-chr17:46123931..46126830,2	MCF-7	breast:
15	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
16	chr17:46048621..46053225-chr17:46056317..46060413,5	K562	blood:
17	chr17:45971907..45976557-chr17:46046916..46050358,7	K562	blood:
18	chr17:46047439..46051573-chr17:46055956..46059590,5	MCF-7	breast:
19	chr17:46048370..46050701-chr17:46124898..46126529,2	K562	blood:
20	chr17:45971907..45974928-chr17:46046916..46050084,5	K562	blood:
21	chr17:46048142..46050112-chr17:46183426..46185210,2	K562	blood:

No data

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000141295	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000108424	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000002919	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11079799	0.82[JPT][hapmap]
rs11871969	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs16948424	1.00[YRI][hapmap]
rs2074185	0.82[JPT][hapmap]
rs3805364	1.00[CHB][hapmap]
rs3805366	1.00[CHB][hapmap]
rs4793688	0.82[JPT][hapmap]
rs4793741	0.85[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794224	0.82[JPT][hapmap]
rs4794318	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4794333	0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs73323378	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8071778	1.00[CHB][hapmap]
rs8082043	0.93[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs886444	0.93[CHD][hapmap];0.85[JPT][hapmap];0.91[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	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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17617010	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs17617010	SCRN2	cis	Esophagus Mucosa	GTEx
rs17617010	SCRN2	cis	Esophagus Muscularis	GTEx
rs17617010	SCRN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46047600-46049600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr17:46047800-46050000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr17:46048000-46049600	Active TSS	HSMMtube	muscle
4	chr17:46048000-46049800	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr17:46048600-46049600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr17:46048600-46049800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr17:46048600-46049800	Flanking Active TSS	Liver	Liver
8	chr17:46048600-46049800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr17:46048600-46050000	Flanking Active TSS	Dnd41	blood
10	chr17:46048800-46049600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
11	chr17:46048800-46049600	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr17:46048800-46049600	Flanking Active TSS	HepG2	liver
13	chr17:46048800-46050000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr17:46049000-46049600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:46049000-46049600	Enhancers	Primary hematopoietic stem cells	blood
16	chr17:46049000-46049600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr17:46049000-46049600	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr17:46049000-46049600	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr17:46049000-46049600	Enhancers	Fetal Heart	heart
20	chr17:46049000-46049600	Flanking Active TSS	Osteobl	bone
21	chr17:46049000-46049800	Enhancers	Primary T cells from cord blood	blood
22	chr17:46049000-46049800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr17:46049000-46050000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr17:46049000-46050000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr17:46049000-46050000	Enhancers	Fetal Brain Male	brain
26	chr17:46049000-46050000	Enhancers	Spleen	Spleen
27	chr17:46049000-46050400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr17:46049000-46050400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr17:46049000-46050400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr17:46049000-46050800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr17:46049000-46050800	Weak transcription	Gastric	stomach
32	chr17:46049000-46051000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr17:46049000-46051200	Weak transcription	Aorta	Aorta
34	chr17:46049000-46051600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr17:46049000-46052200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:46049000-46055200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr17:46049000-46056000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr17:46049200-46049600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr17:46049200-46049600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr17:46049200-46049600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr17:46049200-46049600	Enhancers	Primary B cells from cord blood	blood
42	chr17:46049200-46049600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:46049200-46049600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr17:46049200-46049600	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr17:46049200-46049600	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr17:46049200-46049600	Flanking Active TSS	Fetal Intestine Large	intestine
47	chr17:46049200-46049600	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr17:46049200-46049600	Enhancers	Psoas Muscle	Psoas
49	chr17:46049200-46049600	Enhancers	Thymus	Thymus
50	chr17:46049200-46049600	Flanking Active TSS	HMEC	breast

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