Variant report

Variant	rs9609538
Chromosome Location	chr22:32809832-32809833
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:73)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:73 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr22:32809765-32810044	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr22:32809820-32809970	GM12801	blood:	n/a	n/a
3	CTCF	chr22:32809812-32810015	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr22:32809820-32809970	AoAF	blood vessel:	n/a	n/a
5	RAD21	chr22:32809731-32810167	HCT-116	colon:	n/a	n/a
6	CTCF	chr22:32809705-32810056	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr22:32809800-32809950	NHDF-neo	bronchial:	n/a	n/a
8	SMC3	chr22:32809795-32810094	GM12878	blood:	n/a	n/a
9	CTCF	chr22:32809820-32809970	HFF-Myc	foreskin:	n/a	n/a
10	CTCF	chr22:32809800-32809950	HPAF	blood vessel:	n/a	n/a
11	CTCF	chr22:32809780-32809930	GM12866	blood:	n/a	n/a
12	RAD21	chr22:32809827-32810062	HepG2	liver:	n/a	n/a
13	CTCF	chr22:32809820-32809970	WI-38	lung:	n/a	n/a
14	CTCF	chr22:32809668-32810248	SK-N-SH	brain:	n/a	n/a
15	CTCF	chr22:32809807-32810042	HUVEC	blood vessel:	n/a	n/a
16	RAD21	chr22:32809682-32810271	SK-N-SH	brain:	n/a	n/a
17	CTCF	chr22:32809820-32809970	HPF	lung:	n/a	n/a
18	CTCF	chr22:32809828-32809999	A549	lung:	n/a	n/a
19	CTCF	chr22:32809820-32809970	GM12878	blood:	n/a	n/a
20	CTCF	chr22:32809820-32809970	HEK293	kidney:	n/a	n/a
21	RAD21	chr22:32809757-32810096	IMR90	lung:	n/a	n/a
22	CTCF	chr22:32809820-32809970	HCT-116	colon:	n/a	n/a
23	SMC3	chr22:32809830-32810051	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr22:32809820-32809970	K562	blood:	n/a	n/a
25	RAD21	chr22:32809812-32810100	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr22:32809723-32810138	A549	lung:	n/a	n/a
27	CTCF	chr22:32809780-32809930	GM12872	blood:	n/a	n/a
28	CTCF	chr22:32809800-32809950	GM12875	blood:	n/a	n/a
29	CTCF	chr22:32809737-32810143	MCF-7	breast:	n/a	n/a
30	CTCF	chr22:32809780-32809930	A549	lung:	n/a	n/a
31	SMC3	chr22:32809771-32810372	SK-N-SH	brain:	n/a	n/a
32	CTCF	chr22:32809801-32810039	K562	blood:	n/a	n/a
33	CTCF	chr22:32809827-32810032	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr22:32809745-32809998	T-47D	breast:	n/a	n/a
35	NR2F2	chr22:32809793-32810002	K562	blood:	n/a	n/a
36	ZNF143	chr22:32809829-32810049	GM12878	blood:	n/a	n/a
37	RAD21	chr22:32809800-32810095	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr22:32809820-32809970	HA-sp	spinal cord:	n/a	n/a
39	CTCF	chr22:32809820-32809970	GM12874	blood:	n/a	n/a
40	RAD21	chr22:32809806-32810131	SK-N-SH_RA	brain:	n/a	n/a
41	RAD21	chr22:32809809-32810181	MCF-7	breast:	n/a	n/a
42	FOXA2	chr22:32809807-32810038	HepG2	liver:	n/a	n/a
43	SMC3	chr22:32809781-32810129	HepG2	liver:	n/a	n/a
44	CTCF	chr22:32809761-32810113	K562	blood:	n/a	n/a
45	CTCF	chr22:32809780-32809930	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr22:32809809-32810039	HepG2	liver:	n/a	n/a
47	CTCF	chr22:32809820-32809970	HRPEpiC	eye:	n/a	n/a
48	CTCF	chr22:32809800-32809950	WERI-Rb-1	eye:	n/a	n/a
49	CTCF	chr22:32809800-32809950	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr22:32809820-32809970	HEEpiC	esophagus:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:32806505..32810377-chr22:32871743..32874140,3	K562	blood:
2	chr22:32808877..32811425-chr22:32872228..32873793,2	K562	blood:
3	22:32292186-32294405..22:32809335-32812035	Hela-S3	cervix:
4	22:32477762-32487457..22:32809335-32812035	Hela-S3	cervix:
5	chr22:32809495..32810013-chr22:32840062..32840817,2	MCF-7	breast:
6	22:32012966-32043914..22:32809335-32812035	Hela-S3	cervix:
7	22:32809335-32812035..22:32872511-32874561	Hela-S3	cervix:
8	22:32188129-32210582..22:32809335-32812035	Hela-S3	cervix:
9	22:32809335-32812035..22:32860159-32865649	H1-hESC	embryonic stem cell:	embryo
10	chr22:32809030..32810169-chr22:32839774..32840840,4	MCF-7	breast:
11	22:32334260-32338420..22:32809335-32812035	K562	blood:
12	22:32809335-32812035..22:32868055-32872511	Hela-S3	cervix:
13	chr22:32807562..32810232-chr22:32869269..32871220,2	K562	blood:
14	22:32053085-32061138..22:32809335-32812035	Hela-S3	cervix:
15	22:32809335-32812035..22:33452523-33459358	Hela-S3	cervix:

No data

Variant related genes	Relation type
RTCB	TF binding region
ENSG00000100170	Chromatin interaction
ENSG00000128254	Chromatin interaction
ENSG00000100150	Chromatin interaction
ENSG00000100225	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000184459	Chromatin interaction
ENSG00000241878	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2072817	0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs2076042	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2076044	0.90[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.95[ASN][1000 genomes]
rs2281036	0.96[YRI][hapmap]
rs2413114	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749421	0.96[YRI][hapmap]
rs5749426	0.83[YRI][hapmap]
rs5754066	0.96[YRI][hapmap]
rs715629	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609537	1.00[ASW][hapmap];0.91[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9619262	0.88[CHD][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459874	chr22:32574274-32866934	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv588895	chr22:32574274-32866934	Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1064737	chr22:32603912-32829725	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1066118	chr22:32779078-32815334	Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1055701	chr22:32806595-32845403	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9609538	PLA2G3	cis	cerebellum	SCAN
rs9609538	THOC5	cis	cerebellum	SCAN
rs9609538	C22orf28	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32808200-32818000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr22:32808400-32818000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:32808600-32810000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr22:32808800-32810000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr22:32808800-32810000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr22:32808800-32810000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr22:32808800-32810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr22:32808800-32810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr22:32808800-32810200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr22:32808800-32810600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr22:32809000-32810000	Weak transcription	HMEC	breast
12	chr22:32809000-32810000	Weak transcription	NHEK	skin
13	chr22:32809000-32814000	Weak transcription	GM12878-XiMat	blood
14	chr22:32809000-32817600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr22:32809200-32810000	Weak transcription	Liver	Liver
16	chr22:32809600-32810600	Enhancers	K562	blood

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