Variant report

Variant	rs6504833
Chromosome Location	chr17:45396087-45396088
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr17:45395867-45396239	MCF-7	breast:	n/a	n/a
2	CTCF	chr17:45396042-45396127	MCF-7	breast:	n/a	n/a
3	CTCF	chr17:45396040-45396190	GM12871	blood:	n/a	n/a
4	RAD21	chr17:45395932-45396295	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr17:45396014-45396146	GM13977	blood:	n/a	n/a
6	CTCF	chr17:45396040-45396190	GM12865	blood:	n/a	n/a
7	CTCF	chr17:45395980-45396130	GM12873	blood:	n/a	n/a
8	CTCF	chr17:45395980-45396130	WERI-Rb-1	eye:	n/a	n/a
9	CTCF	chr17:45396020-45396170	GM12865	blood:	n/a	n/a
10	CTCF	chr17:45396015-45396150	GM12878	blood:	n/a	n/a
11	CTCF	chr17:45396000-45396236	GM12878	blood:	n/a	n/a
12	CTCF	chr17:45395982-45396189	MCF-7	breast:	n/a	n/a
13	RAD21	chr17:45395928-45396271	HepG2	liver:	n/a	n/a
14	JUND	chr17:45396068-45396277	HepG2	liver:	n/a	n/a
15	CTCF	chr17:45396020-45396170	GM12869	blood:	n/a	n/a
16	CTCF	chr17:45396020-45396170	MCF-7	breast:	n/a	n/a
17	CTCF	chr17:45396080-45396230	K562	blood:	n/a	n/a
18	CTCF	chr17:45396000-45396150	GM12873	blood:	n/a	n/a
19	CTCF	chr17:45396034-45396152	HepG2	liver:	n/a	n/a
20	CTCF	chr17:45395967-45396250	HepG2	liver:	n/a	n/a
21	CTCF	chr17:45396019-45396147	GM12892	blood:	n/a	n/a
22	RAD21	chr17:45395926-45396235	HepG2	liver:	n/a	n/a
23	CTCF	chr17:45396030-45396130	GM10266	blood:	n/a	n/a
24	CTCF	chr17:45395980-45396130	GM12872	blood:	n/a	n/a
25	RAD21	chr17:45395969-45396214	GM12878	blood:	n/a	n/a
26	ARID3A	chr17:45396060-45396189	HepG2	liver:	n/a	n/a
27	CTCF	chr17:45396040-45396190	HepG2	liver:	n/a	n/a
28	CTCF	chr17:45395970-45396203	MCF-7	breast:	n/a	n/a
29	CTCF	chr17:45395980-45396130	GM12865	blood:	n/a	n/a
30	CTCF	chr17:45396060-45396210	GM06990	blood:	n/a	n/a
31	CTCF	chr17:45395980-45396130	GM12875	blood:	n/a	n/a
32	CTCF	chr17:45396070-45396175	K562	blood:	n/a	n/a
33	CTCF	chr17:45395960-45396110	GM12867	blood:	n/a	n/a
34	CTCF	chr17:45396020-45396170	GM12872	blood:	n/a	n/a
35	RAD21	chr17:45395872-45396323	HepG2	liver:	n/a	n/a
36	CTCF	chr17:45396060-45396210	WERI-Rb-1	eye:	n/a	n/a
37	CTCF	chr17:45395980-45396130	HepG2	liver:	n/a	n/a
38	CTCF	chr17:45396057-45396104	NHEK	skin:	n/a	n/a
39	TAL1	chr17:45396035-45396088	K562	blood:	n/a	n/a
40	CTCF	chr17:45396000-45396150	GM12870	blood:	n/a	n/a
41	CTCF	chr17:45395940-45396090	GM12866	blood:	n/a	n/a
42	CTCF	chr17:45396020-45396170	GM12864	blood:	n/a	n/a
43	CTCF	chr17:45396000-45396150	GM12871	blood:	n/a	n/a
44	CTCF	chr17:45396035-45396131	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr17:45396040-45396116	MCF-7	breast:	n/a	n/a
46	CTCF	chr17:45396044-45396110	MCF-7	breast:	n/a	n/a
47	CTCF	chr17:45396080-45396230	MCF-7	breast:	n/a	n/a
48	SMC3	chr17:45395949-45396238	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:45302596..45304693-chr17:45393589..45396501,2	MCF-7	breast:
2	chr17:45295037..45297924-chr17:45394687..45396289,2	K562	blood:
3	chr17:45302015..45304122-chr17:45394820..45397251,2	K562	blood:

No data

Variant related genes	Relation type
EFCAB13	TF binding region
ENSG00000198336	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1000232	0.80[YRI][hapmap]
rs11079772	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs11650072	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11655943	0.85[YRI][hapmap]
rs11658426	0.82[EUR][1000 genomes]
rs12600865	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2271803	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs2317677	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34589418	0.82[EUR][1000 genomes]
rs35161461	0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs35435669	0.82[EUR][1000 genomes]
rs35983484	0.81[EUR][1000 genomes]
rs3809863	0.86[YRI][hapmap]
rs3809865	0.80[EUR][1000 genomes]
rs4968314	0.82[EUR][1000 genomes]
rs4968316	0.80[EUR][1000 genomes]
rs6504836	0.82[EUR][1000 genomes]
rs7218813	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs7221232	0.80[EUR][1000 genomes]
rs7225700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068200	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8075410	0.82[EUR][1000 genomes]
rs9303534	0.82[EUR][1000 genomes]
rs9893410	0.82[EUR][1000 genomes]
rs9894860	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9899121	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9912450	0.81[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6504833	C17orf57	cis	cerebellum	SCAN
rs6504833	C17orf57	cis	parietal	SCAN
rs6504833	NBR1	cis	parietal	SCAN
rs6504833	RAB5C	cis	parietal	SCAN
rs6504833	KRT33A	cis	parietal	SCAN
rs6504833	VPS25	cis	cerebellum	SCAN
rs6504833	G6PC	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45357200-45398000	Weak transcription	Psoas Muscle	Psoas
2	chr17:45382800-45400800	Weak transcription	Lung	lung
3	chr17:45388400-45398000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr17:45388800-45400800	Weak transcription	Aorta	Aorta
5	chr17:45391200-45400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr17:45393000-45398000	Weak transcription	Fetal Muscle Leg	muscle
7	chr17:45393000-45398200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:45393000-45400600	Weak transcription	Brain Angular Gyrus	brain
9	chr17:45393200-45400600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr17:45393200-45400600	Weak transcription	Colon Smooth Muscle	Colon
11	chr17:45393200-45400600	Weak transcription	Fetal Heart	heart
12	chr17:45393200-45400600	Weak transcription	Pancreas	Pancrea
13	chr17:45393600-45398000	Weak transcription	Fetal Stomach	stomach
14	chr17:45393600-45398400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:45394200-45400600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr17:45394200-45400600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr17:45394400-45400000	Weak transcription	HUVEC	blood vessel
18	chr17:45394600-45398400	Weak transcription	Adipose Nuclei	Adipose
19	chr17:45394800-45399800	Weak transcription	Hela-S3	cervix
20	chr17:45394800-45400200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr17:45394800-45400400	Weak transcription	NH-A	brain
22	chr17:45394800-45400600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr17:45394800-45400600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr17:45395000-45400000	Weak transcription	NHDF-Ad	bronchial
25	chr17:45395200-45400600	Weak transcription	Fetal Intestine Small	intestine
26	chr17:45395200-45400600	Weak transcription	Osteobl	bone
27	chr17:45395400-45396800	Enhancers	HepG2	liver
28	chr17:45395600-45396200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr17:45395800-45396200	ZNF genes & repeats	A549	lung
30	chr17:45395800-45396400	Enhancers	Primary hematopoietic stem cells	blood
31	chr17:45396000-45396200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr17:45396000-45396200	Genic enhancers	HSMMtube	muscle

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