Variant report

Variant	rs9609537
Chromosome Location	chr22:32807769-32807770
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	USF2	chr22:32807685-32807870	Hela-S3	cervix:	n/a	n/a
2	RELA	chr22:32807450-32808564	GM19099	blood:	n/a	n/a
3	POLR2A	chr22:32807246-32808452	HepG2	liver:	n/a	n/a
4	CTCF	chr22:32807740-32807990	AoAF	blood vessel:	n/a	n/a
5	HCFC1	chr22:32807542-32808919	Hela-S3	cervix:	n/a	n/a
6	TCF7L2	chr22:32807577-32808532	PANC-1	pancreas:	n/a	chr22:32808175-32808189
7	HA-E2F1	chr22:32807569-32808512	MCF-7	breast:	n/a	chr22:32808239-32808248
8	MAX	chr22:32807636-32808248	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr22:32807427-32808420	MCF10A-Er-Src	breast:	n/a	n/a
10	TBP	chr22:32807600-32808502	GM12878	blood:	n/a	n/a
11	CTCF	chr22:32807760-32807910	HMEC	breast:	n/a	n/a
12	FOSL2	chr22:32807433-32807848	HepG2	liver:	n/a	chr22:32807646-32807653 chr22:32807644-32807656 chr22:32807645-32807656 chr22:32807646-32807654 chr22:32807647-32807658 chr22:32807646-32807654
13	POLR2A	chr22:32807371-32808396	GM12891	blood:	n/a	n/a
14	CTCF	chr22:32807760-32807910	WERI-Rb-1	eye:	n/a	n/a
15	FOS	chr22:32807507-32807837	MCF10A-Er-Src	breast:	n/a	chr22:32807646-32807653 chr22:32807644-32807656 chr22:32807645-32807656 chr22:32807646-32807654 chr22:32807647-32807658 chr22:32807646-32807654
16	SMC3	chr22:32807688-32808375	Hela-S3	cervix:	n/a	chr22:32807840-32807848
17	POLR2A	chr22:32807368-32808226	HepG2	liver:	n/a	n/a
18	POU2F2	chr22:32807432-32807839	GM12878	blood:	n/a	n/a
19	POLR2A	chr22:32807768-32808574	HepG2	liver:	n/a	n/a
20	FOS	chr22:32807478-32807832	MCF10A-Er-Src	breast:	n/a	chr22:32807646-32807653 chr22:32807644-32807656 chr22:32807645-32807656 chr22:32807646-32807654 chr22:32807647-32807658 chr22:32807646-32807654
21	MXI1	chr22:32807404-32808455	GM12878	blood:	n/a	n/a
22	MAX	chr22:32807725-32807939	K562	blood:	n/a	n/a
23	JUND	chr22:32807490-32807818	HepG2	liver:	n/a	chr22:32807646-32807653 chr22:32807644-32807656 chr22:32807645-32807656 chr22:32807646-32807654 chr22:32807644-32807655 chr22:32807647-32807658 chr22:32807646-32807654
24	KAP1	chr22:32807498-32808601	HEK293	kidney:	n/a	n/a
25	MAX	chr22:32807572-32808438	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr22:32807432-32807788	MCF10A-Er-Src	breast:	n/a	n/a
27	MAX	chr22:32807601-32808226	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr22:32807265-32808438	GM12878	blood:	n/a	n/a
29	MAX	chr22:32807769-32808403	A549	lung:	n/a	n/a
30	TBP	chr22:32807615-32808470	HepG2	liver:	n/a	n/a
31	CTCF	chr22:32807760-32807910	GM12866	blood:	n/a	n/a
32	POLR2A	chr22:32807289-32807783	GM12891	blood:	n/a	n/a
33	MXI1	chr22:32807486-32808441	Hela-S3	cervix:	n/a	n/a
34	FOS	chr22:32807478-32807837	MCF10A-Er-Src	breast:	n/a	chr22:32807646-32807653 chr22:32807644-32807656 chr22:32807645-32807656 chr22:32807646-32807654 chr22:32807647-32807658 chr22:32807646-32807654
35	POLR2A	chr22:32807640-32808513	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr22:32807403-32808604	GM12891	blood:	n/a	n/a
37	MXI1	chr22:32807144-32808972	SK-N-SH	brain:	n/a	n/a
38	MAX	chr22:32807644-32808519	A549	lung:	n/a	n/a
39	TCF7L2	chr22:32807684-32808437	HCT-116	colon:	n/a	chr22:32808175-32808189
40	SIN3AK20	chr22:32807704-32808523	HCT-116	colon:	n/a	n/a
41	PML	chr22:32807348-32808538	GM12878	blood:	n/a	n/a
42	SIN3AK20	chr22:32807737-32808363	HepG2	liver:	n/a	n/a
43	CTCF	chr22:32807700-32807850	K562	blood:	n/a	n/a
44	POLR2A	chr22:32807719-32808444	GM12892	blood:	n/a	n/a
45	MAX	chr22:32807584-32808418	Hela-S3	cervix:	n/a	n/a
46	ELF1	chr22:32807758-32808459	GM12878	blood:	n/a	n/a
47	SIN3A	chr22:32807065-32808475	H1-hESC	embryonic stem cell:	n/a	n/a
48	JUND	chr22:32807468-32807825	H1-hESC	embryonic stem cell:	n/a	chr22:32807646-32807653 chr22:32807644-32807656 chr22:32807645-32807656 chr22:32807646-32807654 chr22:32807644-32807655 chr22:32807647-32807658 chr22:32807646-32807654
49	ARID3A	chr22:32807476-32807814	HepG2	liver:	n/a	n/a
50	TCF7L2	chr22:32807027-32808862	HEK293	kidney:	n/a	chr22:32808175-32808189 chr22:32807213-32807220

No.	Distal block	Cell Line	Cell type
1	chr22:32806505..32810377-chr22:32871743..32874140,3	K562	blood:
2	chr22:32803479..32806391-chr22:32807402..32809274,3	MCF-7	breast:
3	chr22:32802183..32805062-chr22:32805761..32809013,3	MCF-7	breast:
4	chr22:32806637..32808324-chr22:32870497..32872790,2	MCF-7	breast:
5	chr22:32801191..32803610-chr22:32806296..32808272,2	K562	blood:
6	chr22:32778843..32780459-chr22:32807463..32809458,2	K562	blood:
7	chr22:32807562..32810232-chr22:32869269..32871220,2	K562	blood:
8	chr22:32806622..32809672-chr22:32869373..32872144,4	MCF-7	breast:

Variant related genes	Relation type
RTCB	TF binding region
ENSG00000100225	Chromatin interaction
ENSG00000100220	Chromatin interaction
ENSG00000241954	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2072817	0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs2076042	0.96[CEU][hapmap];0.80[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2076044	0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs2281036	1.00[YRI][hapmap]
rs2413114	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56923835	0.82[ASN][1000 genomes]
rs5749421	1.00[YRI][hapmap]
rs5749426	0.88[YRI][hapmap]
rs5754063	0.84[YRI][hapmap]
rs5754066	1.00[YRI][hapmap]
rs715629	0.93[ASW][hapmap];0.96[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609538	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	0.84[CHD][hapmap];0.84[JPT][hapmap];0.91[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
rs9609537	C22orf28	cis	cerebellum	SCAN
rs9609537	THOC5	cis	cerebellum	SCAN
rs9609537	PLA2G3	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32806200-32807800	Flanking Active TSS	Duodenum Mucosa	Duodenum
2	chr22:32806400-32807800	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr22:32806400-32808600	Active TSS	Colonic Mucosa	Colon
4	chr22:32806400-32808600	Active TSS	Fetal Kidney	kidney
5	chr22:32806400-32808800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr22:32806600-32807800	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr22:32806600-32807800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr22:32806600-32808400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr22:32806600-32808600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr22:32806600-32809000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr22:32806800-32807800	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr22:32806800-32807800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr22:32806800-32808000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr22:32806800-32808000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr22:32806800-32808400	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr22:32806800-32808800	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr22:32807000-32807800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr22:32807000-32807800	Flanking Active TSS	Placenta	Placenta
19	chr22:32807000-32808000	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr22:32807000-32808400	Active TSS	H9 Cell Line	embryonic stem cell
21	chr22:32807000-32808400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr22:32807000-32808400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr22:32807000-32808600	Active TSS	Aorta	Aorta
24	chr22:32807000-32808800	Active TSS	Left Ventricle	heart
25	chr22:32807000-32808800	Active TSS	Psoas Muscle	Psoas
26	chr22:32807200-32807800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr22:32807200-32808000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr22:32807200-32808200	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr22:32807200-32808400	Active TSS	H1 Cell Line	embryonic stem cell
30	chr22:32807200-32808400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr22:32807200-32808400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr22:32807200-32808400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr22:32807200-32808400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr22:32807200-32808400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr22:32807200-32808400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr22:32807200-32808400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr22:32807200-32808400	Active TSS	Placenta Amnion	Placenta Amnion
38	chr22:32807200-32808400	Active TSS	GM12878-XiMat	blood
39	chr22:32807200-32808400	Active TSS	HSMM	muscle
40	chr22:32807200-32808400	Active TSS	NH-A	brain
41	chr22:32807200-32808600	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr22:32807200-32808600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr22:32807200-32808600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr22:32807200-32808600	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr22:32807200-32808600	Active TSS	Fetal Intestine Large	intestine
46	chr22:32807200-32808600	Active TSS	Fetal Intestine Small	intestine
47	chr22:32807200-32808600	Active TSS	Fetal Muscle Trunk	muscle
48	chr22:32807200-32808600	Active TSS	Pancreas	Pancrea
49	chr22:32807200-32808600	Active TSS	A549	lung
50	chr22:32807200-32808600	Active TSS	K562	blood

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