Variant report

Variant	rs9366717
Chromosome Location	chr6:28191057-28191058
allele	C/T
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28184931..28189194-chr6:28190077..28194573,12	MCF-7	breast:
2	chr6:28182735..28195387-chr6:28315960..28325841,32	K562	blood:
3	chr6:28188764..28191744-chr6:28301995..28304592,2	MCF-7	breast:
4	chr6:28184789..28191313-chr6:28230652..28235913,7	K562	blood:
5	chr6:28189695..28192033-chr6:28349571..28352462,4	K562	blood:
6	chr6:28186460..28191177-chr6:28246836..28252039,7	K562	blood:
7	chr6:28047206..28049069-chr6:28188430..28191262,2	K562	blood:
8	chr6:28127881..28130043-chr6:28189652..28192231,2	K562	blood:
9	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
10	chr6:28100317..28107200-chr6:28184436..28191088,8	MCF-7	breast:
11	chr6:28102806..28106129-chr6:28190797..28194598,4	K562	blood:
12	chr6:28102723..28113786-chr6:28183725..28194756,41	K562	blood:
13	chr6:28184339..28187958-chr6:28190844..28194750,7	MCF-7	breast:
14	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:
15	chr6:28163458..28166230-chr6:28188324..28191413,3	K562	blood:
16	chr6:28190987..28192829-chr6:28194559..28196499,2	MCF-7	breast:
17	chr6:28108043..28113786-chr6:28190485..28194607,10	K562	blood:
18	chr6:28188391..28191172-chr6:28347437..28349201,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000226314	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000272009	Chromatin interaction
ENSG00000197279	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000137185	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10456362	0.93[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs1076639	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11755032	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11965538	0.93[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs13200462	0.93[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs1321505	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1339899	1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1419183	0.93[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs1679709	0.93[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs1679732	0.93[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs16893735	1.00[YRI][hapmap]
rs17720293	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs1778507	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.85[ASN][1000 genomes]
rs1778508	0.93[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs1778511	0.93[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs1936365	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs213239	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs213241	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs213243	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs213244	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs2743554	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs2743555	0.81[EUR][1000 genomes]
rs2799077	0.93[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs2799079	0.93[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[EUR][1000 genomes]
rs34130214	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34712084	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3734571	0.90[YRI][hapmap]
rs3757188	0.82[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs4713138	1.00[YRI][hapmap]
rs4713139	0.82[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4713140	0.82[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs68141011	0.81[EUR][1000 genomes]
rs6901575	0.93[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap]
rs6920512	1.00[CHB][hapmap];0.90[YRI][hapmap];0.84[ASN][1000 genomes]
rs735765	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs7740487	0.81[EUR][1000 genomes]
rs8180562	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs853676	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs853678	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs853679	0.82[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs853681	0.83[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs853685	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs853687	0.90[CHB][hapmap]
rs9295765	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9295766	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9295767	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9368561	0.80[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9380051	0.81[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs9380064	0.82[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9380069	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs9393902	0.81[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs9393908	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461432	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9461446	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs9461448	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9461449	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9468287	0.82[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9468300	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9468321	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs9468322	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs9468342	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs9468345	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs9986596	0.80[EUR][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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
2	esv2634712	chr6:28189671-28191361	Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs9366717	ZNF192	cis	cerebellum	SCAN
rs9366717	ZSCAN23	cis	cerebellum	SCAN
rs9366717	BTN3A2	trans	lymphoblastoid	seeQTL
rs9366717	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs9366717	HIST1H4L	cis	parietal	SCAN
rs9366717	LRRC16A	cis	parietal	SCAN
rs9366717	ZNF323	cis	parietal	SCAN
rs9366717	AL022393.7	cis	Muscle Skeletal	GTEx
rs9366717	ABT1	cis	parietal	SCAN
rs9366717	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs9366717	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs9366717	ZSCAN23	cis	parietal	SCAN
rs9366717	ZNF192P1	cis	Heart Left Ventricle	GTEx
rs9366717	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28186600-28192400	Weak transcription	Spleen	Spleen
2	chr6:28187000-28192400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:28187000-28192400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:28187200-28192000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:28187200-28192000	Weak transcription	HMEC	breast
6	chr6:28187200-28192200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:28187400-28192000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:28187400-28192000	Weak transcription	Hela-S3	cervix
9	chr6:28188200-28191200	Weak transcription	Placenta	Placenta
10	chr6:28188600-28192400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:28188800-28192000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:28188800-28192000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:28190000-28192400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:28190200-28192000	Weak transcription	K562	blood
15	chr6:28190800-28192200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:28191000-28192000	Weak transcription	NHEK	skin
17	chr6:28191000-28192200	Weak transcription	HUVEC	blood vessel

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