Variant report

Variant	rs174761
Chromosome Location	chr22:29702139-29702140
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	EP300	chr22:29701937-29702572	ECC-1	luminal epithelium:	n/a	chr22:29702293-29702309 chr22:29702299-29702315 chr22:29702257-29702273 chr22:29702283-29702299
2	MAX	chr22:29702057-29702625	A549	lung:	n/a	n/a
3	GATA3	chr22:29701935-29703097	MCF-7	breast:	n/a	n/a
4	E2F6	chr22:29702075-29702924	K562	blood:	n/a	chr22:29702318-29702325 chr22:29702316-29702327 chr22:29702318-29702325 chr22:29702318-29702325 chr22:29702885-29702894
5	MAX	chr22:29702127-29703191	SK-N-SH	brain:	n/a	chr22:29702885-29702895
6	POLR2A	chr22:29702050-29702931	PBDE	blood:	n/a	n/a
7	MAZ	chr22:29702058-29703657	Hela-S3	cervix:	n/a	chr22:29702885-29702895
8	CTCF	chr22:29702113-29702502	GM12878	blood:	n/a	chr22:29702302-29702315
9	YY1	chr22:29701966-29702624	ECC-1	luminal epithelium:	n/a	chr22:29702231-29702242
10	MAX	chr22:29702131-29702428	HepG2	liver:	n/a	n/a
11	RCOR1	chr22:29702007-29702558	Hela-S3	cervix:	n/a	n/a
12	MAX	chr22:29701922-29703739	A549	lung:	n/a	chr22:29702885-29702895
13	EP300	chr22:29702124-29703272	K562	blood:	n/a	chr22:29702293-29702309 chr22:29702299-29702315 chr22:29702257-29702273 chr22:29702914-29702930 chr22:29702283-29702299
14	RAD21	chr22:29702060-29702550	HepG2	liver:	n/a	chr22:29702296-29702310 chr22:29702303-29702316 chr22:29702295-29702309 chr22:29702300-29702319 chr22:29702305-29702315
15	YY1	chr22:29701953-29702484	HepG2	liver:	n/a	chr22:29702231-29702242
16	TCF12	chr22:29701819-29703578	ECC-1	luminal epithelium:	n/a	chr22:29702870-29702878 chr22:29702992-29703000 chr22:29702074-29702084
17	MAZ	chr22:29702080-29703349	K562	blood:	n/a	chr22:29702885-29702895
18	YY1	chr22:29702043-29702499	A549	lung:	n/a	chr22:29702231-29702242
19	SIN3A	chr22:29702095-29703026	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr22:29702090-29703706	SK-N-MC	brain:	n/a	n/a
21	HCFC1	chr22:29701861-29703393	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr22:29701983-29703175	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr22:29702131-29702453	A549	lung:	n/a	n/a
24	CTCF	chr22:29702020-29702170	HBMEC	blood vessel:	n/a	n/a
25	MYC	chr22:29702103-29702335	HUVEC	blood vessel:	n/a	n/a
26	SMC3	chr22:29702068-29702617	Hela-S3	cervix:	n/a	chr22:29702301-29702315 chr22:29702305-29702315
27	MAX	chr22:29702046-29703418	Hela-S3	cervix:	n/a	chr22:29702885-29702895
28	CTBP2	chr22:29702009-29703073	H1-hESC	embryonic stem cell:	n/a	n/a
29	YY1	chr22:29702106-29702391	HepG2	liver:	n/a	chr22:29702231-29702242
30	CTCF	chr22:29702095-29702523	IMR90	lung:	n/a	chr22:29702302-29702315
31	POLR2A	chr22:29702054-29702592	HUVEC	blood vessel:	n/a	n/a
32	CTCF	chr22:29701947-29703979	SK-N-SH	brain:	n/a	chr22:29702302-29702315
33	JUN	chr22:29701948-29702230	H1-hESC	embryonic stem cell:	n/a	chr22:29702105-29702112
34	MYC	chr22:29702053-29702648	NB4	blood:	n/a	n/a
35	ZNF384	chr22:29701988-29702308	K562	blood:	n/a	n/a
36	MAX	chr22:29702075-29703196	SK-N-SH	brain:	n/a	chr22:29702885-29702895
37	RAD21	chr22:29702120-29702609	MCF-7	breast:	n/a	chr22:29702296-29702310 chr22:29702303-29702316 chr22:29702295-29702309 chr22:29702300-29702319 chr22:29702305-29702315
38	HA-E2F1	chr22:29702076-29703218	Hela-S3	cervix:	n/a	chr22:29702318-29702325 chr22:29702256-29702267 chr22:29702999-29703008 chr22:29702318-29702325 chr22:29702318-29702325 chr22:29702885-29702894
39	HDAC2	chr22:29702071-29702657	MCF-7	breast:	n/a	n/a
40	GTF3C2	chr22:29701905-29702254	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr22:29702000-29702620	K562	blood:	n/a	chr22:29702302-29702315
42	MAX	chr22:29702063-29703162	MCF-7	breast:	n/a	chr22:29702885-29702895
43	MAX	chr22:29701917-29703687	HepG2	liver:	n/a	chr22:29702885-29702895
44	KAP1	chr22:29701971-29702746	HEK293	kidney:	n/a	n/a
45	MAX	chr22:29701829-29703686	ECC-1	luminal epithelium:	n/a	chr22:29702885-29702895
46	POLR2A	chr22:29702138-29702445	A549	lung:	n/a	n/a
47	YY1	chr22:29702024-29702720	SK-N-SH	brain:	n/a	chr22:29702231-29702242
48	CTCF	chr22:29702116-29702423	SK-N-SH_RA	brain:	n/a	chr22:29702302-29702315
49	HNF4G	chr22:29702015-29702443	HepG2	liver:	n/a	n/a
50	TBP	chr22:29702076-29703096	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29661955..29666922-chr22:29700529..29704114,10	K562	blood:
2	chr12:49658305..49660610-chr22:29700972..29702617,2	K562	blood:
3	chr22:29660929..29666447-chr22:29700529..29705135,9	K562	blood:
4	chr22:29700857..29704420-chr22:29708764..29712339,6	MCF-7	breast:
5	chr22:29685583..29688004-chr22:29700889..29703726,2	MCF-7	breast:
6	chr22:29670501..29673200-chr22:29700972..29703163,2	K562	blood:
7	chr22:29701804..29704290-chr22:29781998..29785634,5	MCF-7	breast:

Variant related genes	Relation type
GAS2L1	TF binding region
ENSG00000100280	Chromatin interaction
ENSG00000100263	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000100276	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000182944	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11090564	0.81[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs131180	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs131182	0.89[ASN][1000 genomes]
rs131189	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs140062	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs140063	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs140066	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs174759	0.96[ASN][1000 genomes]
rs174762	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.80[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs174764	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs174765	0.91[ASN][1000 genomes]
rs174766	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs174767	0.82[ASN][1000 genomes]
rs174769	0.88[ASN][1000 genomes]
rs174770	0.87[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs174771	0.88[ASN][1000 genomes]
rs2071578	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2072051	0.87[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2267132	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs2267133	0.80[ASW][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs2283849	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2283850	0.87[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2301290	1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2301291	0.80[JPT][hapmap]
rs2301585	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2519486	0.84[ASN][1000 genomes]
rs2857462	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2857466	0.89[JPT][hapmap]
rs28755	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3788410	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3788411	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4820803	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs4820804	0.87[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5752903	0.87[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs5763138	1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs5763139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763178	0.88[ASN][1000 genomes]
rs6006090	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6006098	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs715494	0.87[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs737883	0.80[JPT][hapmap]
rs762817	0.81[ASN][1000 genomes]
rs879580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs909798	0.84[JPT][hapmap]
rs9537	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs98069	0.81[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][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	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv829154	chr22:29617485-29724001	Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv829155	chr22:29664396-29724001	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv914959	chr22:29696438-29712874	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv914960	chr22:29696438-29714069	Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs174761	GAS2L1	cis	putamen	BrainEAC
rs174761	GAS2L1	cis	occipital cortex	BrainEAC
rs174761	GAS2L1	cis	brain	BrainEAC
rs174761	PITPNB	cis	cerebellum	SCAN
rs174761	GAS2L1	cis	frontal cortex	BrainEAC

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29670600-29702400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr22:29695800-29702200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr22:29696200-29702400	Weak transcription	Aorta	Aorta
4	chr22:29697200-29702200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr22:29697200-29702600	Weak transcription	Small Intestine	intestine
6	chr22:29697400-29702400	Weak transcription	NHLF	lung
7	chr22:29699200-29702400	Weak transcription	HSMMtube	muscle
8	chr22:29699600-29702400	Weak transcription	Colon Smooth Muscle	Colon
9	chr22:29699800-29702600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr22:29701200-29702200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr22:29701400-29702200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
12	chr22:29701400-29702200	Enhancers	Brain Anterior Caudate	brain
13	chr22:29701400-29702200	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr22:29701400-29702200	Enhancers	Placenta	Placenta
15	chr22:29701600-29702200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
16	chr22:29701600-29702200	Enhancers	Fetal Muscle Trunk	muscle
17	chr22:29701600-29702400	Enhancers	Spleen	Spleen
18	chr22:29701800-29702200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr22:29701800-29702200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr22:29702000-29702200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr22:29702000-29702200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
22	chr22:29702000-29702200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr22:29702000-29702200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr22:29702000-29702200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr22:29702000-29702200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr22:29702000-29702200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr22:29702000-29702200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr22:29702000-29702200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr22:29702000-29702200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr22:29702000-29702200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr22:29702000-29702200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr22:29702000-29702200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr22:29702000-29702200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr22:29702000-29702200	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr22:29702000-29702200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr22:29702000-29702200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr22:29702000-29702200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr22:29702000-29702200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr22:29702000-29702200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
40	chr22:29702000-29702200	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr22:29702000-29702200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr22:29702000-29702200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
43	chr22:29702000-29702200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
44	chr22:29702000-29702200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr22:29702000-29702200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
46	chr22:29702000-29702200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr22:29702000-29702200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
48	chr22:29702000-29702200	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
49	chr22:29702000-29702200	Flanking Bivalent TSS/Enh	Primary T killer memory cells from peripheral blood	blood
50	chr22:29702000-29702200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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