Variant report

Variant	rs9468015
Chromosome Location	chr6:27198718-27198719
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:15)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27100701..27102362-chr6:27197500..27199646,2	K562	blood:
2	chr6:27192498..27195500-chr6:27198039..27200217,4	K562	blood:
3	chr6:27196971..27199808-chr6:27204338..27205850,2	MCF-7	breast:
4	chr6:27192383..27194653-chr6:27197243..27199028,2	MCF-7	breast:
5	chr6:27197426..27201736-chr6:27203200..27207154,7	K562	blood:
6	chr6:27198164..27199852-chr6:27213905..27216503,2	K562	blood:
7	chr6:27114077..27118449-chr6:27196059..27200185,5	K562	blood:
8	chr6:27195411..27200167-chr6:27200252..27206108,10	K562	blood:
9	chr6:27196755..27199547-chr6:27440103..27442239,2	K562	blood:
10	chr6:27198348..27200537-chr6:27219109..27221018,2	MCF-7	breast:
11	chr6:27197041..27202373-chr6:27261458..27267425,7	K562	blood:
12	chr6:27197164..27198769-chr6:27245728..27247415,2	K562	blood:
13	chr6:27129888..27131649-chr6:27195657..27199036,3	K562	blood:
14	chr6:27198091..27199769-chr6:27253992..27255811,2	K562	blood:
15	chr6:27198224..27199922-chr6:27229756..27232749,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POM121L2-1	chr6:27198606-27199041	expReg_chr6_1853_-

No data

Variant related genes	Relation type
ENSG00000096654	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10946904	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1102564	0.83[CHD][hapmap]
rs1156086	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13194053	0.81[YRI][hapmap]
rs13219181	0.81[YRI][hapmap]
rs2142686	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2295603	0.84[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs28594674	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800309	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800312	0.87[GIH][hapmap]
rs3800314	0.83[ASN][1000 genomes]
rs3823427	0.93[YRI][hapmap]
rs4236043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4546474	0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4713072	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713074	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5030956	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6902268	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6904071	0.81[YRI][hapmap]
rs6912503	0.86[GIH][hapmap]
rs6913660	0.81[YRI][hapmap]
rs6916555	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6917311	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940384	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759741	0.86[YRI][hapmap]
rs926300	0.81[YRI][hapmap]
rs9379968	0.82[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs9468009	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468010	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468013	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs996247	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9468015	HIST1H2AL	cis	cerebellum	SCAN
rs9468015	ZNF323	cis	parietal	SCAN
rs9468015	ZSCAN23	cis	cerebellum	SCAN
rs9468015	ZNF391	cis	cerebellum	SCAN
rs9468015	BTN3A3	cis	cerebellum	SCAN
rs9468015	ZNF184	cis	parietal	SCAN
rs9468015	ZNF323	cis	cerebellum	SCAN
rs9468015	BTN3A2	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27196200-27199800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:27196800-27199600	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:27196800-27200200	Active TSS	A549	lung
4	chr6:27197000-27199200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:27197000-27199400	Active TSS	H1 Cell Line	embryonic stem cell
6	chr6:27197000-27199600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:27197000-27199600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:27197000-27200400	Active TSS	K562	blood
9	chr6:27197200-27199000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:27197200-27199000	Active TSS	NHEK	skin
11	chr6:27197200-27199200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:27197200-27199400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:27197200-27199400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:27197400-27198800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:27197400-27198800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:27197400-27198800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:27197400-27199000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:27197400-27199400	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr6:27197400-27199400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:27197400-27199600	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr6:27197400-27199600	Active TSS	Placenta	Placenta
22	chr6:27197400-27199800	Active TSS	H9 Cell Line	embryonic stem cell
23	chr6:27197600-27198800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:27197600-27199400	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr6:27198000-27199200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:27198200-27198800	Active TSS	HSMM	muscle
27	chr6:27198200-27199800	Active TSS	Hela-S3	cervix
28	chr6:27198400-27198800	Active TSS	HSMMtube	muscle
29	chr6:27198400-27199600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr6:27198600-27198800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:27198600-27198800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:27198600-27198800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:27198600-27198800	Bivalent Enhancer	Fetal Intestine Small	intestine
34	chr6:27198600-27198800	Bivalent Enhancer	Small Intestine	intestine
35	chr6:27198600-27198800	Enhancers	GM12878-XiMat	blood
36	chr6:27198600-27198800	Flanking Bivalent TSS/Enh	HepG2	liver
37	chr6:27198600-27198800	Flanking Active TSS	HMEC	breast
38	chr6:27198600-27198800	Flanking Active TSS	Osteobl	bone
39	chr6:27198600-27199000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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