Variant report

Variant	rs12409549
Chromosome Location	chr1:47784311-47784312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:58)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:58 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:47784258-47784400	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr1:47784246-47784417	MCF-7	breast:	n/a	n/a
3	CTCF	chr1:47784209-47784428	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr1:47784068-47784461	K562	blood:	n/a	n/a
5	CTCF	chr1:47784212-47784446	K562	blood:	n/a	n/a
6	CTCF	chr1:47784220-47784370	HPAF	blood vessel:	n/a	n/a
7	CTCF	chr1:47784240-47784390	K562	blood:	n/a	n/a
8	CTCF	chr1:47784252-47784427	Gliobla	brain:	n/a	n/a
9	CTCF	chr1:47784248-47784410	K562	blood:	n/a	n/a
10	CTCF	chr1:47784260-47784410	K562	blood:	n/a	n/a
11	CTCF	chr1:47784272-47784384	Medullo	brain:	n/a	n/a
12	CTCF	chr1:47784251-47784429	MCF-7	breast:	n/a	n/a
13	CTCF	chr1:47784141-47784435	HepG2	liver:	n/a	n/a
14	CTCF	chr1:47784280-47784430	A549	lung:	n/a	n/a
15	CTCF	chr1:47784258-47784408	A549	lung:	n/a	n/a
16	CTCF	chr1:47784178-47784426	K562	blood:	n/a	n/a
17	CTCF	chr1:47784302-47784388	SK-N-SH_RA	brain:	n/a	n/a
18	CTCF	chr1:47784280-47784430	HBMEC	blood vessel:	n/a	n/a
19	CTCF	chr1:47784220-47784370	HMF	breast:	n/a	n/a
20	CTCF	chr1:47784260-47784410	AG09309	skin:	n/a	n/a
21	CTCF	chr1:47784254-47784418	GM19238	blood:	n/a	n/a
22	CTCF	chr1:47784260-47784410	WERI-Rb-1	eye:	n/a	n/a
23	CTCF	chr1:47784260-47784410	SK-N-SH_RA	brain:	n/a	n/a
24	CTCF	chr1:47784284-47784395	NHEK	skin:	n/a	n/a
25	YY1	chr1:47784258-47784437	K562	blood:	n/a	n/a
26	CTCF	chr1:47784200-47784450	GM12868	blood:	n/a	n/a
27	CTCF	chr1:47784251-47784425	MCF-7	breast:	n/a	n/a
28	CTCF	chr1:47784280-47784430	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr1:47784244-47784425	MCF-7	breast:	n/a	n/a
30	CTCF	chr1:47784300-47784450	GM12871	blood:	n/a	n/a
31	CTCF	chr1:47784240-47784390	GM12874	blood:	n/a	n/a
32	CTCF	chr1:47784253-47784402	HepG2	liver:	n/a	n/a
33	CTCF	chr1:47784282-47784377	HUVEC	blood vessel:	n/a	n/a
34	CTCF	chr1:47784260-47784410	HepG2	liver:	n/a	n/a
35	CTCF	chr1:47784253-47784421	GM12891	blood:	n/a	n/a
36	CTCF	chr1:47784260-47784410	GM12878	blood:	n/a	n/a
37	CTCF	chr1:47784310-47784382	LNCaP	prostate:	n/a	n/a
38	CTCF	chr1:47784272-47784408	H1-hESC	embryonic stem cell:	n/a	n/a
39	PAX5	chr1:47784189-47784400	GM12878	blood:	n/a	n/a
40	CTCF	chr1:47784299-47784409	GM19240	blood:	n/a	n/a
41	CTCF	chr1:47784284-47784362	GM10248	blood:	n/a	n/a
42	CTCF	chr1:47784262-47784392	MCF-7	breast:	n/a	n/a
43	CTCF	chr1:47784200-47784350	HCT-116	colon:	n/a	n/a
44	CTCF	chr1:47784250-47784381	Spleen_OC	spleen:	n/a	n/a
45	CTCF	chr1:47784240-47784390	HEEpiC	esophagus:	n/a	n/a
46	CTCF	chr1:47784262-47784402	GM12878	blood:	n/a	n/a
47	CTCF	chr1:47784221-47784437	K562	blood:	n/a	n/a
48	CTCF	chr1:47784260-47784410	HCPEpiC	choroid plexus:	n/a	n/a
49	CTCF	chr1:47784261-47784422	GM10266	blood:	n/a	n/a
50	RCOR1	chr1:47784203-47784384	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47778166..47781558-chr1:47781655..47786926,8	K562	blood:
2	chr1:47776996..47781717-chr1:47782920..47788458,9	K562	blood:

No data

Variant related genes	Relation type
STIL	TF binding region
ENSG00000123473	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10157883	0.86[ASN][1000 genomes]
rs1028646	0.85[ASN][1000 genomes]
rs1028647	0.85[ASN][1000 genomes]
rs10789507	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10890475	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10890476	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10890477	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10890478	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211504	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211508	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211513	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211517	0.80[ASN][1000 genomes]
rs11211520	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211521	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11211522	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11211523	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211524	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11578038	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11582877	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12024163	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12039726	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12040451	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12042624	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12046294	0.94[EUR][1000 genomes]
rs12047319	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12048407	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12566521	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2306470	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2406105	0.86[ASN][1000 genomes]
rs2472730	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2472731	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2494247	0.85[ASN][1000 genomes]
rs2742099	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2742103	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742104	0.86[ASN][1000 genomes]
rs2758735	0.85[ASN][1000 genomes]
rs2758736	0.83[ASN][1000 genomes]
rs2758737	0.85[ASN][1000 genomes]
rs2758744	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2821087	0.85[ASN][1000 genomes]
rs2821088	0.85[ASN][1000 genomes]
rs2821089	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2821090	0.85[ASN][1000 genomes]
rs2821092	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2897237	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3088062	0.87[ASN][1000 genomes]
rs3122607	0.87[ASN][1000 genomes]
rs3122611	0.85[ASN][1000 genomes]
rs3122615	0.87[ASN][1000 genomes]
rs3122616	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3122619	0.86[ASN][1000 genomes]
rs3122620	0.88[ASN][1000 genomes]
rs3122623	0.85[ASN][1000 genomes]
rs3125630	0.82[ASN][1000 genomes]
rs3125631	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3125632	0.88[ASN][1000 genomes]
rs3125635	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3125636	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3125638	0.81[ASN][1000 genomes]
rs3125641	0.86[ASN][1000 genomes]
rs3125644	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35880845	0.88[ASN][1000 genomes]
rs3923691	0.83[AMR][1000 genomes]
rs3925058	0.88[ASN][1000 genomes]
rs4463720	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4492666	0.88[ASN][1000 genomes]
rs4926836	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4926839	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56987466	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58688029	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59492977	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61284456	0.87[EUR][1000 genomes]
rs61782712	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61782733	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61784774	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6588348	0.82[ASN][1000 genomes]
rs6660321	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6671254	0.86[ASN][1000 genomes]
rs6697248	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7511699	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525650	0.82[ASN][1000 genomes]
rs7532148	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541522	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7541748	0.88[ASN][1000 genomes]
rs7545281	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9436394	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9436429	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9436430	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9436749	0.86[ASN][1000 genomes]
rs9436882	0.88[ASN][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	esv3390574	chr1:47778981-47803091	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47780200-47798400	Weak transcription	Spleen	Spleen
2	chr1:47780600-47798000	Weak transcription	HSMMtube	muscle
3	chr1:47780800-47789200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:47780800-47791200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:47780800-47797800	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:47782800-47784400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:47783200-47785400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:47783800-47787800	Weak transcription	HepG2	liver
9	chr1:47784000-47784600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:47784000-47785000	Weak transcription	K562	blood

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