Variant report

Variant	rs6909960
Chromosome Location	chr6:28688921-28688922
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28686790..28690321-chr6:28972014..28975051,3	K562	blood:
2	chr6:28688275..28691006-chr6:28830286..28833046,2	K562	blood:
3	chr6:28452420..28454018-chr6:28686803..28689231,2	K562	blood:
4	chr6:28686813..28689115-chr6:28758010..28760174,2	K562	blood:
5	chr6:28688047..28690834-chr6:28847432..28849865,2	K562	blood:
6	chr6:28687184..28689466-chr6:28889833..28891936,2	K562	blood:
7	chr6:28682762..28689665-chr6:28860684..28866524,9	K562	blood:
8	chr6:28685695..28690739-chr6:28709794..28719692,17	K562	blood:
9	chr6:28685640..28691299-chr6:28719887..28724041,7	K562	blood:
10	chr6:28688164..28689744-chr6:28726401..28728148,2	K562	blood:
11	chr6:28687184..28690282-chr6:28725684..28728661,4	K562	blood:
12	chr6:28686780..28689583-chr6:28731850..28734136,2	K562	blood:
13	chr6:28687492..28689983-chr6:28961733..28963921,2	K562	blood:
14	chr6:28687246..28689887-chr6:28948960..28952398,3	K562	blood:
15	chr6:27797995..27799606-chr6:28688387..28690532,2	K562	blood:
16	chr6:28579298..28581830-chr6:28687615..28690190,2	K562	blood:
17	chr6:27804984..27807620-chr6:28688259..28689782,2	K562	blood:
18	chr6:28579345..28581830-chr6:28688286..28691469,3	K562	blood:
19	chr6:28687938..28689790-chr6:28777726..28779382,2	K562	blood:
20	chr6:28655903..28659289-chr6:28687482..28691877,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000224157	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000184348	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000197914	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10498733	1.00[AFR][1000 genomes]
rs1107160	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17280797	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17280818	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17281186	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17346574	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1891757	0.97[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1936180	1.00[AFR][1000 genomes]
rs3999045	0.95[AMR][1000 genomes]
rs55641015	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55659253	1.00[AMR][1000 genomes]
rs55764335	1.00[AMR][1000 genomes]
rs55891766	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs56003969	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs56098960	1.00[AMR][1000 genomes]
rs56165011	1.00[AMR][1000 genomes]
rs56296645	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56384403	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57170714	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57693980	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57748269	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs57791058	1.00[AMR][1000 genomes]
rs57965355	1.00[AMR][1000 genomes]
rs58104924	1.00[AFR][1000 genomes]
rs58238888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58258185	1.00[AMR][1000 genomes]
rs59233561	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs59475656	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs59959723	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs60252686	1.00[AMR][1000 genomes]
rs60311527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61094745	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61208746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61657599	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61703239	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6901325	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905871	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6906105	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6906506	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916286	0.95[AMR][1000 genomes]
rs6923795	1.00[AMR][1000 genomes]
rs7738101	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742889	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7748319	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7751451	1.00[AMR][1000 genomes]
rs7751884	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7754365	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755641	1.00[AFR][1000 genomes]
rs7758798	1.00[AMR][1000 genomes]
rs7760656	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7765829	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7766599	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7772111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7772373	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7772482	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7772682	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9688414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9767343	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9767359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6909960	ZNF323	cis	parietal	SCAN
rs6909960	FAM65B	cis	cerebellum	SCAN
rs6909960	ZNF323	cis	cerebellum	SCAN
rs6909960	ZSCAN23	cis	cerebellum	SCAN
rs6909960	ZKSCAN3	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28687200-28689000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr6:28687200-28689200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:28687400-28689000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:28687600-28689200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr6:28687600-28689200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:28688000-28689000	Flanking Active TSS	HepG2	liver
7	chr6:28688000-28689200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:28688800-28689000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
9	chr6:28688800-28689400	Enhancers	K562	blood

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