Variant report

Variant	rs12102776
Chromosome Location	chr16:31166028-31166029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr16:31165782-31166063	Hela-S3	cervix:	n/a	n/a
2	TCF7L2	chr16:31165797-31166270	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr16:31165758-31166175	Hela-S3	cervix:	n/a	n/a
4	BRCA1	chr16:31165804-31166090	Hela-S3	cervix:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31165273..31167495-chr16:31190173..31191698,2	K562	blood:
2	chr16:31163570..31167428-chr16:31190002..31192096,4	MCF-7	breast:
3	chr16:31153578..31155721-chr16:31165072..31166722,2	MCF-7	breast:
4	chr16:31164437..31166721-chr16:31189439..31192571,4	MCF-7	breast:
5	chr16:31165839..31168639-chr16:31188061..31189958,2	K562	blood:
6	chr16:31157987..31161829-chr16:31166001..31169725,4	K562	blood:
7	chr16:31155383..31157939-chr16:31165219..31167593,2	K562	blood:
8	chr16:31163863..31166773-chr16:31190173..31192747,2	K562	blood:

No data

Variant related genes	Relation type
PRSS36	TF binding region
ENSG00000178226	Chromatin interaction
ENSG00000089280	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1060506	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs10871454	0.92[CHD][hapmap]
rs11150604	0.92[CHD][hapmap]
rs11862744	0.92[CHD][hapmap]
rs11865038	0.82[CHB][hapmap]
rs11865499	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs12597511	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs14235	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs1549293	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs1978487	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs2032915	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs2303222	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs2359612	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs2855475	0.82[CHB][hapmap]
rs35468353	0.92[CHD][hapmap]
rs3751855	0.82[CHB][hapmap]
rs4468641	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs4527034	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs4889623	1.00[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap]
rs4889625	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57611503	0.87[ASN][1000 genomes]
rs6565217	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs7190802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7196726	0.82[CHB][hapmap]
rs7197717	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs7199949	0.82[CHB][hapmap]
rs7294	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs732172	0.92[CHD][hapmap]
rs749670	0.82[CHB][hapmap]
rs749671	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs749767	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs750952	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs8050894	0.82[CHB][hapmap]
rs881929	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs889548	0.82[CHB][hapmap]
rs889555	0.84[CHD][hapmap]
rs9923231	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs9934438	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs9936329	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs9939286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9939417	0.92[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
4	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
5	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
6	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
7	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
8	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
9	esv1797877	chr16:30948643-31188432	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
10	nsv905740	chr16:31066249-31232437	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
11	nsv905741	chr16:31066249-31247924	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
12	nsv905742	chr16:31102321-31247924	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	188 gene(s)	inside rSNPs	diseases
13	nsv542900	chr16:31137352-31197027	Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
14	esv987713	chr16:31163107-31173998	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12102776	ITGAX	cis	multi-tissue	Pritchard
rs12102776	MYST1	cis	cerebellum	SCAN
rs12102776	FUS	cis	cerebellum	SCAN
rs12102776	YPEL3	cis	parietal	SCAN
rs12102776	MYST1	cis	parietal	SCAN
rs12102776	MYST1	Cis_1M	lymphoblastoid	RTeQTL
rs12102776	C16orf93	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31154400-31190400	Weak transcription	Right Atrium	heart
2	chr16:31162000-31171200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:31163000-31168200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr16:31163000-31168200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr16:31163000-31168600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr16:31163400-31168200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr16:31163800-31168400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr16:31163800-31168400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr16:31166000-31168800	Weak transcription	Hela-S3	cervix

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