Variant report

Variant	rs9393908
Chromosome Location	chr6:28190830-28190831
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28190810-28190860	HRCEpiC	kidney:	n/a
2	chr6:28190810-28190860	GM12878	blood:	n/a
3	chr6:28190810-28190860	PrEC	prostate:	n/a
4	chr6:28190810-28190860	U87	brain:	n/a
5	chr6:28190810-28190860	HRPEpiC	eye:	n/a
6	chr6:28190810-28190860	GM12891	blood:	n/a
7	chr6:28190810-28190860	SAEC	small airway:	n/a
8	chr6:28190810-28190860	K562	blood:	n/a
9	chr6:28190810-28190860	IMR90	lung:	fetal
10	chr6:28190810-28190860	SKMC	muscle:	n/a
11	chr6:28190810-28190860	SK-N-SH	brain:	n/a
12	chr6:28190810-28190860	HAEpiC	amniotic membrane:	n/a
13	chr6:28190810-28190860	HUVEC	blood vessel:	n/a
14	chr6:28190810-28190860	NT2-D1	testis:	n/a
15	chr6:28190810-28190860	HEEpiC	esophagus:	n/a
16	chr6:28190810-28190860	PFSK-1	brain:	n/a
17	chr6:28190810-28190860	ProgFib	skin:	n/a
18	chr6:28190810-28190860	HPAEpiC	pulmonary alveolar:	n/a
19	chr6:28190810-28190860	NB4	blood:	n/a
20	chr6:28190810-28190860	HMEC	breast:	n/a
21	chr6:28190810-28190860	GM19239	blood:	n/a
22	chr6:28190810-28190860	AG04450	lung:	fetal
23	chr6:28190810-28190860	Hela-S3	cervix:	n/a
24	chr6:28190810-28190860	AoSMC	blood vessel:	n/a
25	chr6:28190810-28190860	H1-hESC	embryonic stem cell:	embryo
26	chr6:28190810-28190860	Caco-2	colon:	n/a
27	chr6:28190810-28190860	HCF	heart:	n/a
28	chr6:28190810-28190860	AG10803	skin:	n/a
29	chr6:28190810-28190860	RPTEC	kidney:	n/a
30	chr6:28190810-28190860	BE2_C	brain:	n/a
31	chr6:28190810-28190860	Hepatocyte	liver:	n/a
32	chr6:28190810-28190860	GM12892	blood:	n/a
33	chr6:28190810-28190860	HCPEpiC	choroid plexus:	n/a
34	chr6:28190810-28190860	LNCaP	prostate:	n/a
35	chr6:28190810-28190860	SK-N-SH_RA	brain:	n/a
36	chr6:28190810-28190860	HIPEpiC	eye:	n/a
37	chr6:28190810-28190860	AG09309	skin:	n/a
38	chr6:28190810-28190860	NHDF-neo	bronchial:	n/a
39	chr6:28190810-28190860	HepG2	liver:	n/a
40	chr6:28190810-28190860	ECC-1	luminal epithelium:	n/a
41	chr6:28190810-28190860	AG09319	gingival:	n/a
42	chr6:28190810-28190860	AG04449	skin:	fetal
43	chr6:28190810-28190860	BJ	skin:	n/a
44	chr6:28190810-28190860	SK-N-MC	brain:	n/a
45	chr6:28190810-28190860	HL-60	blood:	n/a
46	chr6:28190810-28190860	T-47D	breast:	n/a
47	chr6:28190810-28190860	HCM	heart:	n/a
48	chr6:28190810-28190860	GM06990	blood:	n/a
49	chr6:28190810-28190860	Jurkat	blood:	n/a
50	chr6:28190810-28190860	NHBE	bronchial:	n/a

(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	chr6:28188896..28191056-chr6:28251556..28253787,2	K562	blood:
4	chr6:28188764..28191744-chr6:28301995..28304592,2	MCF-7	breast:
5	chr6:28184789..28191313-chr6:28230652..28235913,7	K562	blood:
6	chr6:28189695..28192033-chr6:28349571..28352462,4	K562	blood:
7	chr6:28186460..28191177-chr6:28246836..28252039,7	K562	blood:
8	chr6:28047206..28049069-chr6:28188430..28191262,2	K562	blood:
9	chr6:28127881..28130043-chr6:28189652..28192231,2	K562	blood:
10	chr6:28183629..28195178-chr6:28316250..28325659,29	K562	blood:
11	chr6:28100317..28107200-chr6:28184436..28191088,8	MCF-7	breast:
12	chr6:28102806..28106129-chr6:28190797..28194598,4	K562	blood:
13	chr6:28102723..28113786-chr6:28183725..28194756,41	K562	blood:
14	chr6:28187110..28190886-chr6:28224658..28229038,5	K562	blood:
15	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:
16	chr6:28163458..28166230-chr6:28188324..28191413,3	K562	blood:
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
TOB2P1	CpG island
ZSCAN9	CpG island
ENSG00000272009	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000189134	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000197279	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10456362	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs1076639	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs11755032	0.90[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs11965538	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs13200462	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs1321505	0.81[CEU][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs1339899	0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs1419183	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs1679709	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs1679732	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs17720293	0.82[EUR][1000 genomes]
rs1778507	0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs1778508	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs1778511	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs1936365	0.88[JPT][hapmap]
rs213239	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs213241	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs213243	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs213244	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2232427	0.81[CEU][hapmap]
rs2743554	0.88[JPT][hapmap]
rs2743555	0.81[EUR][1000 genomes]
rs2799077	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs2799079	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]
rs3757188	0.80[CEU][hapmap];0.92[EUR][1000 genomes]
rs4713139	0.80[CEU][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4713140	0.80[CEU][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs68141011	0.81[EUR][1000 genomes]
rs6901575	0.88[JPT][hapmap]
rs6920512	0.91[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs735765	0.86[EUR][1000 genomes]
rs7740487	0.81[EUR][1000 genomes]
rs8180562	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs853676	0.88[JPT][hapmap]
rs853678	0.88[JPT][hapmap]
rs853679	0.88[JPT][hapmap]
rs853681	0.88[JPT][hapmap]
rs853685	0.88[JPT][hapmap]
rs853687	0.91[CHB][hapmap]
rs9295765	0.91[CHB][hapmap];1.00[JPT][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]
rs9366717	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]
rs9368561	0.80[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9380064	0.80[CEU][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9380069	0.80[CEU][hapmap];0.87[EUR][1000 genomes]
rs9461432	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9461446	0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs9461448	0.90[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs9461449	0.91[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs9468287	0.80[CEU][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9468300	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9468321	0.91[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs9468322	0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs9468342	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs9468345	0.82[CHB][hapmap];0.88[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9393908	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9393908	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs9393908	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs9393908	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs9393908	AL022393.7	cis	Muscle Skeletal	GTEx
rs9393908	ZNF192P1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:16 , 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	chr6:28190400-28191000	Enhancers	NHEK	skin
16	chr6:28190800-28192200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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