Variant report

Variant	rs3796916
Chromosome Location	chr4:106476262-106476263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr4:106476237-106477133	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106471957..106473637-chr4:106475938..106478326,2	MCF-7	breast:
2	chr4:106474325..106476444-chr4:106476458..106478164,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250522	TF binding region
ENSG00000250522	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10026456	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1125254	1.00[YRI][hapmap]
rs1352707	0.89[ASN][1000 genomes]
rs1388040	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1490599	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1490600	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1490601	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1490602	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17035753	0.92[ASN][1000 genomes]
rs17584200	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17839078	0.89[ASN][1000 genomes]
rs2079129	0.82[CEU][hapmap]
rs2189228	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2866798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2866799	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3796917	0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3822274	0.92[ASN][1000 genomes]
rs3960769	0.81[CHB][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.88[ASN][1000 genomes]
rs3974414	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4699186	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4699187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4699188	0.92[ASN][1000 genomes]
rs6533199	1.00[YRI][hapmap]
rs6533204	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6533205	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6817760	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6853877	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7666509	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7672413	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7686705	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9307304	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9307305	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1005011	chr4:106461690-106496019	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1013019	chr4:106461690-106501412	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv524424	chr4:106466128-106491511	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv461610	chr4:106466128-106491511	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv595008	chr4:106466128-106491511	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv517837	chr4:106466588-106502513	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3796916	PPA2	cis	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106470000-106476600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:106472200-106477600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr4:106473400-106476400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr4:106473600-106477400	Active TSS	Duodenum Mucosa	Duodenum
5	chr4:106473600-106477600	Active TSS	Fetal Intestine Large	intestine
6	chr4:106473600-106477600	Weak transcription	Gastric	stomach
7	chr4:106474000-106477400	Weak transcription	Fetal Lung	lung
8	chr4:106474200-106476400	Weak transcription	Placenta	Placenta
9	chr4:106474600-106476600	Weak transcription	Stomach Mucosa	stomach
10	chr4:106474800-106477000	Weak transcription	Fetal Kidney	kidney
11	chr4:106474800-106479400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:106475600-106476600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:106475600-106476800	Enhancers	Pancreas	Pancrea
14	chr4:106476200-106476400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
15	chr4:106476200-106476400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
16	chr4:106476200-106476400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
17	chr4:106476200-106476400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
18	chr4:106476200-106476400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
19	chr4:106476200-106476400	Flanking Active TSS	Fetal Intestine Small	intestine
20	chr4:106476200-106476600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
21	chr4:106476200-106476600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
22	chr4:106476200-106476600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
23	chr4:106476200-106476600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
24	chr4:106476200-106476800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:106476200-106476800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:106476200-106477000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:106476200-106477600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:106476200-106478200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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