Variant report

Variant	rs9609025
Chromosome Location	chr22:31032076-31032077
allele	A/G
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	RAD21	chr22:31030159-31033009	SK-N-SH	brain:	n/a	chr22:31030567-31030586 chr22:31031143-31031156 chr22:31030572-31030584 chr22:31032159-31032171 chr22:31031145-31031157 chr22:31031995-31032005 chr22:31031446-31031456 chr22:31031511-31031524 chr22:31030571-31030580 chr22:31031145-31031155 chr22:31030568-31030582
2	POLR2A	chr22:31030389-31032098	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr22:31030221-31032151	U87	brain:	n/a	n/a
4	CTCF	chr22:31032000-31032150	GM12870	blood:	n/a	n/a
5	MTA3	chr22:31031673-31032326	GM12878	blood:	n/a	n/a
6	POLR2A	chr22:31030277-31032167	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr22:31030291-31032145	U87	brain:	n/a	n/a
8	CCNT2	chr22:31031513-31032077	K562	blood:	n/a	chr22:31031558-31031567
9	ZNF263	chr22:31031725-31032663	HEK293-T-REx	kidney:	n/a	n/a
10	SMC3	chr22:31030099-31032972	SK-N-SH	brain:	n/a	chr22:31032378-31032385 chr22:31031145-31031155 chr22:31031446-31031460 chr22:31031446-31031456 chr22:31030568-31030575 chr22:31030568-31030582 chr22:31032408-31032418
11	EP300	chr22:31030282-31032076	SK-N-SH	brain:	n/a	chr22:31031148-31031157 chr22:31031731-31031740
12	MAZ	chr22:31030211-31032738	IMR90	lung:	n/a	chr22:31031998-31032008 chr22:31030749-31030758
13	NFIC	chr22:31031333-31032175	ECC-1	luminal epithelium:	n/a	n/a
14	MAX	chr22:31031349-31032076	H1-hESC	embryonic stem cell:	n/a	chr22:31031998-31032008
15	REST	chr22:31031471-31032254	H1-neurons	neurons:	n/a	chr22:31031925-31031935
16	HMGN3	chr22:31031343-31032114	K562	blood:	n/a	n/a
17	ZBTB7A	chr22:31030445-31032368	ECC-1	luminal epithelium:	n/a	chr22:31031147-31031156
18	RCOR1	chr22:31030177-31032959	IMR90	lung:	n/a	n/a
19	TCF12	chr22:31031327-31032100	ECC-1	luminal epithelium:	n/a	chr22:31031545-31031553
20	MAX	chr22:31031507-31032208	ECC-1	luminal epithelium:	n/a	chr22:31031998-31032008
21	POLR2A	chr22:31030423-31032124	HUVEC	blood vessel:	n/a	n/a
22	EGR1	chr22:31031371-31032122	HCT-116	colon:	n/a	chr22:31031611-31031625 chr22:31031730-31031740
23	CTCF	chr22:31030137-31032129	SK-N-SH	brain:	n/a	chr22:31030569-31030582 chr22:31031144-31031154 chr22:31030566-31030584 chr22:31031444-31031462 chr22:31030568-31030589 chr22:31031139-31031157 chr22:31030569-31030582 chr22:31031446-31031459 chr22:31030571-31030581 chr22:31030567-31030583 chr22:31031450-31031459 chr22:31030569-31030578
24	ZBTB7A	chr22:31030896-31032346	ECC-1	luminal epithelium:	n/a	chr22:31031147-31031156
25	POLR2A	chr22:31031521-31032077	MCF-7	breast:	n/a	n/a
26	CTCF	chr22:31032020-31032170	AG04449	skin:	n/a	n/a
27	CHD1	chr22:31030212-31033049	IMR90	lung:	n/a	n/a
28	POLR2A	chr22:31031454-31032077	MCF-7	breast:	n/a	n/a
29	POLR2A	chr22:31030322-31032122	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31030552..31033273-chr22:31061698..31065017,4	MCF-7	breast:
2	chr22:31031588..31032094-chr22:31090123..31090949,2	MCF-7	breast:
3	chr22:31030338..31033016-chr22:31062140..31065480,4	MCF-7	breast:

Variant related genes	Relation type
SLC35E4	TF binding region
ENSG00000184792	Chromatin interaction
ENSG00000167065	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs28704032	0.81[EUR][1000 genomes]
rs42942	1.00[CHB][hapmap]
rs5994320	1.00[CHB][hapmap]
rs5994330	1.00[EUR][1000 genomes]
rs5997724	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5997729	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606756	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9606757	0.81[EUR][1000 genomes]
rs9606758	1.00[EUR][1000 genomes]
rs9606763	1.00[EUR][1000 genomes]
rs9609028	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609030	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609033	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv829172	chr22:31024057-31032291	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3374115	chr22:31030477-31033325	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31030600-31032200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr22:31030600-31032400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr22:31030600-31032800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr22:31030600-31032800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr22:31030600-31032800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr22:31030600-31033000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr22:31030600-31033200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr22:31030600-31033200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr22:31030600-31033400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr22:31030600-31033400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr22:31030600-31033400	Flanking Active TSS	Colonic Mucosa	Colon
12	chr22:31030600-31033400	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr22:31030600-31034000	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr22:31030600-31034200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr22:31030600-31034200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr22:31030600-31034400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr22:31030800-31032200	Active TSS	Fetal Kidney	kidney
18	chr22:31030800-31032400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr22:31030800-31032400	Active TSS	Brain Angular Gyrus	brain
20	chr22:31030800-31032400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr22:31030800-31032600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr22:31030800-31032600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr22:31030800-31032600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr22:31030800-31032800	Flanking Active TSS	Brain Germinal Matrix	brain
25	chr22:31030800-31033200	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr22:31030800-31033400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr22:31030800-31033400	Active TSS	Psoas Muscle	Psoas
28	chr22:31030800-31033600	Active TSS	Brain Anterior Caudate	brain
29	chr22:31031000-31032200	Active TSS	Ovary	ovary
30	chr22:31031000-31032800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr22:31031000-31033400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr22:31031000-31033600	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr22:31031200-31032200	Active TSS	Left Ventricle	heart
34	chr22:31031200-31032200	Active TSS	Small Intestine	intestine
35	chr22:31031200-31032400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr22:31031200-31032600	Active TSS	Aorta	Aorta
37	chr22:31031200-31033000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr22:31031200-31033000	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr22:31031200-31033600	Flanking Active TSS	HMEC	breast
40	chr22:31031400-31032200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr22:31031400-31032200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr22:31031400-31032200	Active TSS	Brain Cingulate Gyrus	brain
43	chr22:31031400-31032200	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr22:31031400-31032200	Active TSS	Fetal Brain Female	brain
45	chr22:31031400-31032200	Active TSS	Right Atrium	heart
46	chr22:31031400-31032200	Active TSS	A549	lung
47	chr22:31031400-31032200	Active TSS	GM12878-XiMat	blood
48	chr22:31031400-31032400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr22:31031400-31032600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr22:31031400-31032800	Active TSS	Colon Smooth Muscle	Colon

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