Variant report

Variant	rs3792097
Chromosome Location	chr2:234238784-234238785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr2:234238159-234238956	ECC-1	luminal epithelium:	n/a	chr2:234238581-234238588
2	MAX	chr2:234238301-234238835	ECC-1	luminal epithelium:	n/a	n/a
3	SIN3A	chr2:234238349-234238804	H1-hESC	embryonic stem cell:	n/a	chr2:234238464-234238474
4	NANOG	chr2:234238313-234238816	H1-hESC	embryonic stem cell:	n/a	chr2:234238591-234238600
5	TEAD4	chr2:234238198-234238850	ECC-1	luminal epithelium:	n/a	n/a
6	YY1	chr2:234238281-234238896	ECC-1	luminal epithelium:	n/a	n/a
7	EP300	chr2:234238251-234238858	ECC-1	luminal epithelium:	n/a	chr2:234238267-234238281
8	YY1	chr2:234238247-234238889	H1-hESC	embryonic stem cell:	n/a	n/a
9	YY1	chr2:234238286-234238864	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTBP2	chr2:234238246-234239056	H1-hESC	embryonic stem cell:	n/a	n/a
11	ATF2	chr2:234238270-234238799	H1-hESC	embryonic stem cell:	n/a	n/a
12	NFIC	chr2:234238208-234238933	ECC-1	luminal epithelium:	n/a	n/a
13	TEAD4	chr2:234238149-234239202	ECC-1	luminal epithelium:	n/a	n/a
14	HDAC2	chr2:234238315-234238787	H1-hESC	embryonic stem cell:	n/a	n/a
15	YY1	chr2:234238458-234238879	NT2-D1	testis:	n/a	n/a
16	MAX	chr2:234238257-234238856	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr2:234238317-234238917	ECC-1	luminal epithelium:	n/a	n/a
18	TCF12	chr2:234238078-234239071	ECC-1	luminal epithelium:	n/a	chr2:234238581-234238588
19	TEAD4	chr2:234238403-234238811	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr2:234238318-234238887	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr2:234238299-234239237	ECC-1	luminal epithelium:	n/a	n/a
22	EP300	chr2:234238073-234239096	ECC-1	luminal epithelium:	n/a	chr2:234238267-234238281 chr2:234239048-234239057
23	NFIC	chr2:234238137-234238987	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234238246..234240780-chr2:234263095..234264681,2	K562	blood:
2	chr2:234209576..234212564-chr2:234237690..234239510,2	MCF-7	breast:
3	chr2:234237506..234239939-chr2:234241158..234243320,2	K562	blood:

No data

Variant related genes	Relation type
SAG	TF binding region
ENSG00000243637	Chromatin interaction
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1000547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890336	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891546	0.87[CHB][hapmap]
rs1965811	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241873	0.85[TSI][hapmap]
rs2241874	0.85[TSI][hapmap]
rs2241875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304777	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs3792100	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6431305	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710735	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745476	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6861	0.80[TSI][hapmap]
rs745498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570515	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7608122	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs894100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584699	chr2:234182240-234255547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3792097	GIGYF2	cis	cerebellum	SCAN
rs3792097	ATG16L1	cis	cerebellum	SCAN
rs3792097	ECEL1	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234223600-234245400	Weak transcription	Pancreas	Pancrea
2	chr2:234228400-234240000	Weak transcription	Fetal Intestine Small	intestine
3	chr2:234234400-234239800	Weak transcription	Thymus	Thymus
4	chr2:234237200-234242800	Enhancers	Spleen	Spleen
5	chr2:234237400-234238800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:234237400-234238800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
7	chr2:234237400-234249800	Enhancers	Primary B cells from peripheral blood	blood
8	chr2:234237600-234238800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:234237600-234238800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:234237600-234238800	Enhancers	K562	blood
11	chr2:234237600-234239000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr2:234237600-234239200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
13	chr2:234237600-234239600	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr2:234237800-234238800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:234237800-234239000	Enhancers	H9 Cell Line	embryonic stem cell
16	chr2:234237800-234239600	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr2:234237800-234240000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr2:234237800-234244000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr2:234238000-234238800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr2:234238000-234238800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:234238000-234238800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:234238000-234238800	Enhancers	HSMMtube	muscle
23	chr2:234238000-234239000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:234238000-234239000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:234238000-234239000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
26	chr2:234238000-234239000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:234238000-234239000	Enhancers	HSMM	muscle
28	chr2:234238000-234240000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:234238200-234238800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:234238200-234238800	Enhancers	Lung	lung
31	chr2:234238200-234239000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:234238200-234239000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr2:234238200-234239000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:234238200-234239000	Enhancers	NH-A	brain
35	chr2:234238200-234240000	Enhancers	Primary B cells from cord blood	blood
36	chr2:234238200-234240000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:234238200-234240000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr2:234238200-234240200	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr2:234238400-234238800	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr2:234238400-234238800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:234238400-234238800	Enhancers	HUVEC	blood vessel
42	chr2:234238400-234239800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr2:234238400-234239800	Weak transcription	Fetal Thymus	thymus
44	chr2:234238400-234240000	Enhancers	Primary T cells from cord blood	blood
45	chr2:234238400-234243000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:234238400-234244600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:234238600-234238800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
48	chr2:234238600-234239000	Enhancers	Hela-S3	cervix
49	chr2:234238600-234239600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr2:234238600-234239800	Enhancers	Primary T helper cells PMA-I stimulated	--

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