Variant report

Variant	rs7966795
Chromosome Location	chr12:58031413-58031414
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr12:58031242-58031579	A549	lung:	n/a	n/a
2	CTCF	chr12:58031300-58031450	BJ	skin:	n/a	n/a
3	CTCF	chr12:58031280-58031430	HAc	cerebellar:	n/a	n/a
4	CTCF	chr12:58031380-58031449	Spleen_OC	spleen:	n/a	n/a
5	CTCF	chr12:58031139-58031533	MCF-7	breast:	n/a	n/a
6	CTCF	chr12:58031276-58031562	GM12878	blood:	n/a	n/a
7	CTCF	chr12:58031320-58031470	A549	lung:	n/a	n/a
8	CTCF	chr12:58031300-58031450	HCPEpiC	choroid plexus:	n/a	n/a
9	RAD21	chr12:58031165-58031495	MCF-7	breast:	n/a	n/a
10	CTCF	chr12:58031133-58031593	HCT-116	colon:	n/a	n/a
11	SMC3	chr12:58031367-58031464	GM12878	blood:	n/a	n/a
12	RAD21	chr12:58031218-58031539	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr12:58031082-58031674	MCF-7	breast:	n/a	n/a
14	CTCF	chr12:58031300-58031450	AG04449	skin:	n/a	n/a
15	CTCF	chr12:58031360-58031510	NHDF-neo	bronchial:	n/a	n/a
16	CTCF	chr12:58031280-58031430	AG09319	gingival:	n/a	n/a
17	RAD21	chr12:58031078-58031727	SK-N-SH	brain:	n/a	n/a
18	CTCF	chr12:58031340-58031490	SK-N-SH_RA	brain:	n/a	n/a
19	CTCF	chr12:58031124-58031493	A549	lung:	n/a	n/a
20	CTCF	chr12:58031222-58031479	A549	lung:	n/a	n/a
21	CTCF	chr12:58031301-58031428	HepG2	liver:	n/a	n/a
22	CTCF	chr12:58031380-58031530	NB4	blood:	n/a	n/a
23	RAD21	chr12:58031257-58031524	SK-N-SH_RA	brain:	n/a	n/a
24	CTCF	chr12:58031400-58031550	RPTEC	kidney:	n/a	n/a
25	CTCF	chr12:58031320-58031570	BE2_C	brain:	n/a	n/a
26	CTCF	chr12:58031195-58031418	MCF-7	breast:	n/a	n/a
27	CTCF	chr12:58031280-58031430	HMF	breast:	n/a	n/a
28	CTCF	chr12:58031285-58031535	K562	blood:	n/a	n/a
29	CTCF	chr12:58031300-58031450	HMF	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58030492..58032233-chr12:58033542..58035528,2	K562	blood:
2	chr12:57974514..57977193-chr12:58031041..58032907,2	K562	blood:
3	chr12:57909076..57912703-chr12:58030683..58034118,3	K562	blood:
4	chr12:57908910..57916122-chr12:58022622..58031573,17	K562	blood:
5	chr12:58031339..58033541-chr12:58068001..58070861,2	K562	blood:

No data

Variant related genes	Relation type
B4GALNT1	TF binding region
ENSG00000242990	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000155980	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000208028	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1027315	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1038914	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs1050045	0.88[CEU][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap]
rs12368653	0.86[MEX][hapmap]
rs12371356	0.81[MEX][hapmap]
rs12826708	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12826985	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1552842	0.94[ASN][1000 genomes]
rs1564374	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[ASN][1000 genomes]
rs1873919	0.89[ASN][1000 genomes]
rs2270777	0.84[CEU][hapmap]
rs2277324	0.88[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277326	0.85[MEX][hapmap]
rs2307095	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307097	0.85[MEX][hapmap]
rs2640610	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34271193	0.84[ASN][1000 genomes]
rs6581147	0.83[ASN][1000 genomes]
rs7134861	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7138608	0.81[EUR][1000 genomes]
rs7295422	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7304145	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7311632	0.96[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7952989	0.82[EUR][1000 genomes]
rs799265	0.88[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs903067	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs923828	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv511490	chr12:58026786-58035706	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
5	esv3493502	chr12:58027226-58031438	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	n/a
6	nsv559040	chr12:58028127-58031413	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	n/a
7	esv1802058	chr12:58028127-58062667	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
8	nsv559044	chr12:58028671-58065448	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7966795	FAM119B	cis	cerebellum	SCAN
rs7966795	NCKAP1L	cis	parietal	SCAN
rs7966795	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs7966795	FAM119B	cis	lymphoblastoid	seeQTL
rs7966795	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs7966795	KRT8	cis	cerebellum	SCAN
rs7966795	OR6C4	cis	cerebellum	SCAN
rs7966795	TSPAN31	cis	cerebellum	SCAN
rs7966795	XRCC6BP1	cis	Artery Tibial	GTEx
rs7966795	STAT6	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58027200-58033600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:58027600-58034000	Weak transcription	K562	blood

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