Variant report

Variant	rs34556183
Chromosome Location	chr6:28584775-28584776
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28582156..28586237-chr6:28601069..28603430,3	K562	blood:
2	chr6:28373602..28375467-chr6:28584083..28586880,2	K562	blood:
3	chr6:28556555..28559076-chr6:28582763..28585041,2	K562	blood:
4	chr6:28233569..28236323-chr6:28583574..28585743,2	K562	blood:
5	chr6:28579846..28585618-chr6:28609150..28616432,10	K562	blood:
6	chr6:28366328..28368330-chr6:28583082..28585639,2	K562	blood:
7	chr6:28583985..28585633-chr6:28910730..28913227,2	K562	blood:

Variant related genes	Relation type
ENSG00000197062	Chromatin interaction
ENSG00000232040	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000272278	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000271440	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11963067	0.91[ASN][1000 genomes]
rs11965972	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966966	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11967609	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11970339	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11970409	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13220637	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16894194	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16894197	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16901848	0.88[ASN][1000 genomes]
rs1884936	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1884937	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2394120	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2394121	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2893966	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34020953	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34177106	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34388845	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35466817	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35546888	0.91[ASN][1000 genomes]
rs36069097	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36103239	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4121091	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56389860	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61229539	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6923110	0.91[ASN][1000 genomes]
rs6941188	0.88[ASN][1000 genomes]
rs7741058	0.81[EUR][1000 genomes]
rs7742957	0.88[ASN][1000 genomes]
rs7767008	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7775683	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9357070	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1031671	chr6:28575172-28678126	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs34556183	BTN3A3	cis	parietal	SCAN
rs34556183	ZNF323	cis	parietal	SCAN
rs34556183	LRRC16A	cis	parietal	SCAN
rs34556183	BTN3A3	cis	cerebellum	SCAN
rs34556183	NKAPL	cis	parietal	SCAN
rs34556183	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs34556183	HIST1H2BM	cis	cerebellum	SCAN
rs34556183	ZNF192	cis	cerebellum	SCAN
rs34556183	ZSCAN23	cis	parietal	SCAN
rs34556183	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs34556183	ZKSCAN3	cis	cerebellum	SCAN
rs34556183	ZSCAN23	cis	cerebellum	SCAN
rs34556183	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs34556183	ZKSCAN3	cis	parietal	SCAN
rs34556183	ZNF187	cis	cerebellum	SCAN
rs34556183	HIST1H2BH	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28580800-28585400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:28583600-28584800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:28583600-28584800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:28584200-28585000	Flanking Active TSS	K562	blood
5	chr6:28584400-28584800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:28584400-28586200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:28584400-28588800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:28584600-28584800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:28584600-28589200	Weak transcription	Placenta	Placenta

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