Variant report

Variant	rs9609397
Chromosome Location	chr22:32365973-32365974
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:49)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:49 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr22:32365967-32367117	HCT-116	colon:	n/a	chr22:32366769-32366782 chr22:32366338-32366352
2	ZEB1	chr22:32365854-32367012	GM12878	blood:	n/a	n/a
3	POU2F2	chr22:32365624-32366130	GM12878	blood:	n/a	n/a
4	RAD21	chr22:32365795-32367134	ECC-1	luminal epithelium:	n/a	n/a
5	RAD21	chr22:32365865-32367086	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr22:32365969-32366523	ECC-1	luminal epithelium:	n/a	n/a
7	RAD21	chr22:32365826-32367227	SK-N-SH	brain:	n/a	n/a
8	RAD21	chr22:32365960-32366423	K562	blood:	n/a	n/a
9	RUNX3	chr22:32365721-32366080	GM12878	blood:	n/a	n/a
10	CTCF	chr22:32365942-32367199	MCF-7	breast:	n/a	n/a
11	CTCF	chr22:32365973-32366449	K562	blood:	n/a	n/a
12	ZEB1	chr22:32365957-32367088	HepG2	liver:	n/a	n/a
13	EP300	chr22:32365833-32366332	GM12878	blood:	n/a	n/a
14	CTCF	chr22:32365540-32367361	SK-N-SH	brain:	n/a	n/a
15	MAX	chr22:32365842-32367215	HCT-116	colon:	n/a	n/a
16	CTCF	chr22:32365921-32367205	A549	lung:	n/a	n/a
17	EGR1	chr22:32365950-32367067	HCT-116	colon:	n/a	chr22:32366769-32366782 chr22:32366338-32366352
18	ZNF263	chr22:32365946-32367408	HEK293-T-REx	kidney:	n/a	chr22:32366653-32366662 chr22:32366657-32366678
19	POU2F2	chr22:32365686-32366463	GM12891	blood:	n/a	n/a
20	TCF12	chr22:32365869-32366439	GM12878	blood:	n/a	n/a
21	MAZ	chr22:32365810-32367395	IMR90	lung:	n/a	n/a
22	BHLHE40	chr22:32365913-32366466	K562	blood:	n/a	n/a
23	TCF3	chr22:32365854-32366455	GM12878	blood:	n/a	n/a
24	RAD21	chr22:32365966-32366513	A549	lung:	n/a	n/a
25	RCOR1	chr22:32365860-32366905	GM12878	blood:	n/a	n/a
26	MXI1	chr22:32365877-32366411	GM12878	blood:	n/a	n/a
27	CTCF	chr22:32365840-32365990	BJ	skin:	n/a	n/a
28	BHLHE40	chr22:32365756-32366962	GM12878	blood:	n/a	n/a
29	RAD21	chr22:32365952-32366430	MCF-7	breast:	n/a	n/a
30	RAD21	chr22:32365840-32367203	HCT-116	colon:	n/a	n/a
31	MAX	chr22:32365960-32367161	H1-hESC	embryonic stem cell:	n/a	n/a
32	EP300	chr22:32365840-32366301	GM12878	blood:	n/a	n/a
33	SMC3	chr22:32365869-32367257	SK-N-SH	brain:	n/a	chr22:32366939-32366949
34	MAX	chr22:32365944-32366534	H1-hESC	embryonic stem cell:	n/a	n/a
35	RAD21	chr22:32365901-32367100	A549	lung:	n/a	n/a
36	MTA3	chr22:32365879-32366611	GM12878	blood:	n/a	n/a
37	SMC3	chr22:32365936-32366437	HepG2	liver:	n/a	n/a
38	POU2F2	chr22:32365692-32366018	GM12878	blood:	n/a	n/a
39	RAD21	chr22:32365790-32367236	HCT-116	colon:	n/a	n/a
40	RUNX3	chr22:32365701-32366082	GM12878	blood:	n/a	n/a
41	RAD21	chr22:32365847-32366475	MCF-7	breast:	n/a	n/a
42	RAD21	chr22:32365949-32366448	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAX	chr22:32365867-32367149	MCF-7	breast:	n/a	n/a
44	POU2F2	chr22:32365680-32366112	GM12891	blood:	n/a	n/a
45	SMC3	chr22:32365963-32367021	GM12878	blood:	n/a	chr22:32366939-32366949
46	EP300	chr22:32365849-32366357	GM12878	blood:	n/a	n/a
47	CTCF	chr22:32365970-32366556	MCF-7	breast:	n/a	n/a
48	CTCF	chr22:32365754-32367293	HCT-116	colon:	n/a	n/a
49	RAD21	chr22:32365949-32366478	HepG2	liver:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:62609146..62610653-chr22:32365275..32366775,2	K562	blood:
2	chr22:32365255..32366775-chr3:73159952..73161574,3	K562	blood:
3	chr17:41464701..41467719-chr22:32365255..32368255,4	MCF-7	breast:
4	22:32360288-32405313..22:32764253-32784733	K562	blood:
5	chr22:31952335..31953173-chr22:32365824..32366681,2	MCF-7	breast:
6	chr22:32365255..32368255-chr3:73159964..73161574,3	K562	blood:
7	22:32360288-32405313..22:32868055-32872511	K562	blood:
8	22:32012966-32043914..22:32360288-32405313	K562	blood:
9	chr22:32340998..32345394-chr22:32364660..32368897,5	MCF-7	breast:
10	22:32360288-32405313..22:33452523-33459358	H1-hESC	embryonic stem cell:	embryo
11	chr22:32061316..32062330-chr22:32365767..32366693,3	K562	blood:
12	22:32360288-32405313..22:32750950-32761732	K562	blood:
13	22:32360288-32405313..22:32860159-32865649	K562	blood:
14	chr22:32361170..32363262-chr22:32364167..32366088,2	K562	blood:
15	22:32360288-32405313..22:32740683-32750950	K562	blood:
16	chr22:32268348..32268930-chr22:32365701..32366478,2	MCF-7	breast:
17	chr22:32056838..32059373-chr22:32364593..32366329,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-YWHAH-1	chr22:32365973-32366387	XLOC_014211
2	lnc-YWHAH-1	chr22:32365849-32366387	NONHSAT084924

No data

Variant related genes	Relation type
ENSG00000230866	TF binding region
ENSG00000223247	Chromatin interaction
ENSG00000230736	Chromatin interaction
ENSG00000241954	Chromatin interaction
ENSG00000243519	Chromatin interaction
ENSG00000128276	Chromatin interaction
ENSG00000271093	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000100225	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000184459	Chromatin interaction
ENSG00000128254	Chromatin interaction
ENSG00000128245	Chromatin interaction
ENSG00000232218	Chromatin interaction
ENSG00000205853	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1049583	1.00[YRI][hapmap]
rs1076905	1.00[JPT][hapmap]
rs1076906	1.00[JPT][hapmap]
rs12160839	1.00[JPT][hapmap]
rs12168840	1.00[YRI][hapmap]
rs13053458	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16989716	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2006233	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2006253	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2301415	1.00[YRI][hapmap]
rs2853884	1.00[YRI][hapmap]
rs2853887	1.00[YRI][hapmap]
rs2858750	1.00[YRI][hapmap]
rs4820059	1.00[YRI][hapmap]
rs5994473	1.00[JPT][hapmap]
rs5998234	1.00[JPT][hapmap]
rs5998249	1.00[JPT][hapmap]
rs62240613	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7287435	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7290696	1.00[YRI][hapmap]
rs7291050	1.00[YRI][hapmap]
rs8136636	0.85[EUR][1000 genomes]
rs8138116	1.00[JPT][hapmap]
rs8141011	1.00[YRI][hapmap]
rs8142970	1.00[JPT][hapmap]
rs9606895	0.81[EUR][1000 genomes]
rs9606897	1.00[JPT][hapmap]
rs9606899	1.00[JPT][hapmap]
rs9606900	1.00[JPT][hapmap]
rs9609394	1.00[YRI][hapmap]
rs9609413	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9609421	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9621371	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055450	chr22:32356150-32468832	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1055925	chr22:32358540-32450200	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1063876	chr22:32358540-32463271	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1061546	chr22:32358991-32464350	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1059240	chr22:32362689-32462511	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv544678	chr22:32362689-32462511	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9609397	SCARNA6	trans	lymphoblastoid	seeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32351200-32366000	Weak transcription	Stomach Mucosa	stomach
2	chr22:32351400-32366400	Weak transcription	Right Atrium	heart
3	chr22:32353000-32366000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr22:32353000-32366000	Weak transcription	Esophagus	oesophagus
5	chr22:32353000-32366000	Weak transcription	Gastric	stomach
6	chr22:32353000-32366200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr22:32353400-32366000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr22:32353400-32366400	Weak transcription	Psoas Muscle	Psoas
9	chr22:32354000-32366200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr22:32354200-32366000	Weak transcription	Primary B cells from cord blood	blood
11	chr22:32354400-32366400	Weak transcription	Colonic Mucosa	Colon
12	chr22:32354600-32366000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr22:32354600-32366000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr22:32354600-32366000	Weak transcription	Fetal Lung	lung
15	chr22:32354600-32366200	Weak transcription	Liver	Liver
16	chr22:32354600-32366200	Weak transcription	Brain Angular Gyrus	brain
17	chr22:32354600-32366400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr22:32354600-32366400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr22:32354600-32366400	Weak transcription	NHLF	lung
20	chr22:32354800-32366000	Weak transcription	Brain Germinal Matrix	brain
21	chr22:32354800-32366000	Weak transcription	Osteobl	bone
22	chr22:32354800-32366400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr22:32354800-32366400	Weak transcription	HSMM	muscle
24	chr22:32355000-32366000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr22:32355000-32366000	Weak transcription	Thymus	Thymus
26	chr22:32355000-32366200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr22:32355000-32366200	Weak transcription	NH-A	brain
28	chr22:32355000-32366400	Weak transcription	Left Ventricle	heart
29	chr22:32355000-32366400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr22:32355600-32366000	Weak transcription	Fetal Intestine Small	intestine
31	chr22:32355600-32366200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr22:32357200-32366200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr22:32357800-32366000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr22:32358800-32366200	Weak transcription	Fetal Heart	heart
35	chr22:32360600-32366200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr22:32360800-32366200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr22:32360800-32366200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr22:32360800-32366200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr22:32362000-32366000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr22:32362200-32366200	Weak transcription	Placenta	Placenta
41	chr22:32362600-32366000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr22:32365400-32366000	Enhancers	Primary T cells fromperipheralblood	blood
43	chr22:32365400-32366200	Enhancers	Primary B cells from peripheral blood	blood
44	chr22:32365600-32366000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr22:32365600-32366000	Enhancers	NHEK	skin
46	chr22:32365600-32366200	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr22:32365600-32366200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr22:32365600-32366400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr22:32365600-32366600	Enhancers	Fetal Thymus	thymus
50	chr22:32365800-32366000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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