Variant report

Variant	rs2785601
Chromosome Location	chr1:93487349-93487350
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	CTCF	chr1:93486758-93487621	SK-N-SH	brain:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
2	CTCF	chr1:93487260-93487410	GM12864	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
3	CTCF	chr1:93487220-93487370	HCT-116	colon:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
4	NFE2	chr1:93487195-93487358	GM12878	blood:	n/a	n/a
5	CTCF	chr1:93487240-93487390	WERI-Rb-1	eye:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
6	CTCF	chr1:93487087-93487542	GM12878	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
7	CTCF	chr1:93487131-93487425	MCF-7	breast:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
8	CTCF	chr1:93487260-93487410	NHEK	skin:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
9	CTCF	chr1:93487260-93487410	GM12870	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
10	RAD21	chr1:93487072-93487491	GM12878	blood:	n/a	n/a
11	CTCF	chr1:93487240-93487390	HCFaa	heart:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
12	CTCF	chr1:93487280-93487430	HCM	heart:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
13	RAD21	chr1:93487185-93487399	K562	blood:	n/a	n/a
14	CTCF	chr1:93486973-93487646	HCT-116	colon:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
15	CTCF	chr1:93487240-93487390	Hela-S3	cervix:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
16	CTCF	chr1:93487260-93487410	NHDF-neo	bronchial:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
17	CTCF	chr1:93487211-93487417	GM13976	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
18	RAD21	chr1:93487036-93487577	ECC-1	luminal epithelium:	n/a	n/a
19	CTCF	chr1:93487220-93487370	GM12871	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
20	RAD21	chr1:93487114-93487537	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr1:93487220-93487370	MCF-7	breast:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
22	CTCF	chr1:93487173-93487451	K562	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
23	CTCF	chr1:93487226-93487422	MCF-7	breast:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
24	STAT3	chr1:93487093-93487478	MCF10A-Er-Src	breast:	n/a	n/a
25	CTCF	chr1:93487240-93487390	GM12875	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
26	CTCF	chr1:93487260-93487410	SK-N-SH_RA	brain:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
27	RAD21	chr1:93487206-93487435	K562	blood:	n/a	n/a
28	CTCF	chr1:93487260-93487410	BJ	skin:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
29	RAD21	chr1:93487117-93487537	GM12878	blood:	n/a	n/a
30	CTCF	chr1:93487260-93487410	GM12866	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
31	STAT3	chr1:93486918-93487360	MCF10A-Er-Src	breast:	n/a	n/a
32	SMC3	chr1:93486859-93487534	SK-N-SH	brain:	n/a	n/a
33	CTCF	chr1:93487094-93487474	A549	lung:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
34	CTCF	chr1:93487260-93487410	GM12868	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
35	CTCF	chr1:93487220-93487370	HMEC	breast:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
36	CTCF	chr1:93487220-93487370	AoAF	blood vessel:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
37	CTCF	chr1:93487300-93487450	BE2_C	brain:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
38	CTCF	chr1:93487240-93487390	Caco-2	colon:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
39	CTCF	chr1:93487240-93487390	GM12873	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
40	CTCF	chr1:93487186-93487374	SK-N-SH_RA	brain:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
41	CTCF	chr1:93487003-93487450	Medullo	brain:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
42	CTCF	chr1:93487180-93487437	LNCaP	prostate:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
43	SMC3	chr1:93487115-93487511	HepG2	liver:	n/a	n/a
44	RAD21	chr1:93487047-93487574	A549	lung:	n/a	n/a
45	CTCF	chr1:93487240-93487390	WI-38	lung:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
46	CTCF	chr1:93487280-93487430	GM12873	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
47	CTCF	chr1:93487240-93487390	AG04450	lung:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
48	CTCF	chr1:93487280-93487430	K562	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
49	CTCF	chr1:93487083-93487504	K562	blood:	n/a	chr1:93487307-93487328 chr1:93487305-93487323
50	RAD21	chr1:93486875-93487832	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:93485980..93488495-chr1:93489742..93491453,2	K562	blood:
2	chr1:93486773..93487911-chr1:93527469..93528398,9	K562	blood:
3	chr1:93486837..93487799-chr1:94374760..94375360,2	K562	blood:
4	chr1:93485808..93487588-chr1:93526047..93528280,2	MCF-7	breast:
5	chr1:93486832..93487777-chr1:93527684..93528337,5	MCF-7	breast:
6	chr1:93324004..93325373-chr1:93486850..93487700,5	K562	blood:
7	chr1:93487223..93489014-chr1:93543210..93544783,2	K562	blood:

Variant related genes	Relation type
RN7SKP123	TF binding region
ENSG00000023909	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10874754	1.00[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11164862	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs11164865	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11590314	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12084977	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12091867	0.99[EUR][1000 genomes]
rs12092136	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12094815	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2485031	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs491699	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs569268	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59284207	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61523335	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6657919	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6686863	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6688632	1.00[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74103530	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7536849	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]

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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870775	chr1:93481640-93543119	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2785601	TMED5	cis	parietal	SCAN
rs2785601	KIAA1107	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93474200-93490600	Weak transcription	K562	blood
2	chr1:93480400-93491000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:93482200-93487400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:93482600-93487400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:93486800-93494000	Enhancers	Dnd41	blood
6	chr1:93487000-93487600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr1:93487000-93487600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:93487000-93487600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:93487000-93487600	Enhancers	Liver	Liver
10	chr1:93487200-93488400	Enhancers	Primary B cells from peripheral blood	blood

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