Variant report

Variant	rs3788435
Chromosome Location	chr22:31886954-31886955
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	POLR2A	chr22:31885551-31887032	Raji	blood:	n/a	n/a
2	POLR2A	chr22:31885774-31886985	GM12891	blood:	n/a	n/a
3	SPI1	chr22:31885805-31887037	HL-60	blood:	n/a	chr22:31886582-31886595 chr22:31886582-31886595 chr22:31886585-31886594 chr22:31886583-31886596
4	NFIC	chr22:31885741-31887250	GM12878	blood:	n/a	n/a
5	RUNX3	chr22:31885616-31887150	GM12878	blood:	n/a	n/a
6	WRNIP1	chr22:31886061-31887125	GM12878	blood:	n/a	n/a
7	MEF2A	chr22:31885801-31886976	GM12878	blood:	n/a	n/a
8	POLR2A	chr22:31885039-31886957	GM12878	blood:	n/a	n/a
9	IRF4	chr22:31886079-31887005	GM12878	blood:	n/a	n/a
10	POLR2A	chr22:31885554-31888516	GM12878	blood:	n/a	n/a
11	POLR2A	chr22:31885596-31887110	GM12892	blood:	n/a	n/a
12	POLR2A	chr22:31885696-31887122	GM12878	blood:	n/a	n/a
13	POLR2A	chr22:31884880-31888183	GM12892	blood:	n/a	n/a
14	POLR2A	chr22:31885405-31887044	HUVEC	blood vessel:	n/a	n/a
15	HEY1	chr22:31885831-31886982	K562	blood:	n/a	chr22:31885935-31885950 chr22:31885892-31885907 chr22:31885970-31885985
16	TBL1XR1	chr22:31885688-31887194	GM12878	blood:	n/a	n/a
17	MTA3	chr22:31885852-31887526	GM12878	blood:	n/a	n/a
18	PAX5	chr22:31885616-31886999	GM12878	blood:	n/a	n/a
19	MAX	chr22:31885599-31886966	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr22:31885624-31886963	U87	brain:	n/a	n/a
21	POLR2A	chr22:31886401-31886990	K562	blood:	n/a	n/a
22	STAT5A	chr22:31885685-31887602	GM12878	blood:	n/a	chr22:31885720-31885732 chr22:31886718-31886725
23	EP300	chr22:31885822-31887076	GM12878	blood:	n/a	chr22:31886584-31886598 chr22:31886131-31886147 chr22:31885938-31885954 chr22:31885899-31885908 chr22:31886062-31886078
24	POLR2A	chr22:31884955-31887595	K562	blood:	n/a	n/a
25	EP300	chr22:31885911-31886958	GM12878	blood:	n/a	chr22:31886584-31886598 chr22:31886131-31886147 chr22:31885938-31885954 chr22:31886062-31886078
26	POU2F2	chr22:31885794-31887030	GM12891	blood:	n/a	chr22:31886253-31886260 chr22:31886677-31886687 chr22:31886677-31886687 chr22:31886252-31886261 chr22:31886677-31886686 chr22:31886672-31886690 chr22:31886019-31886031 chr22:31886678-31886685
27	BRCA1	chr22:31886835-31887133	H1-hESC	embryonic stem cell:	n/a	chr22:31886958-31886965
28	RUNX3	chr22:31885536-31887159	GM12878	blood:	n/a	n/a
29	EBF1	chr22:31885958-31886991	GM12878	blood:	n/a	n/a
30	FOXM1	chr22:31885753-31887094	GM12878	blood:	n/a	n/a
31	POLR2A	chr22:31885612-31886987	GM10847	blood:	n/a	n/a
32	ATF2	chr22:31885674-31887011	GM12878	blood:	n/a	n/a
33	POLR2A	chr22:31885618-31886969	U87	brain:	n/a	n/a
34	SPI1	chr22:31886242-31887000	GM12891	blood:	n/a	chr22:31886582-31886595 chr22:31886582-31886595 chr22:31886585-31886594 chr22:31886583-31886596
35	POLR2A	chr22:31885567-31887121	GM12891	blood:	n/a	n/a
36	POLR2A	chr22:31885780-31888630	K562	blood:	n/a	n/a
37	RELA	chr22:31885701-31887113	GM15510	blood:	n/a	n/a
38	STAT5A	chr22:31886139-31886977	GM12878	blood:	n/a	chr22:31886718-31886725
39	CHD2	chr22:31885669-31887027	GM12878	blood:	n/a	chr22:31886026-31886036
40	POLR2A	chr22:31885620-31886959	K562	blood:	n/a	n/a
41	IKZF1	chr22:31886223-31887092	GM12878	blood:	n/a	n/a
42	NRF1	chr22:31885760-31887094	GM12878	blood:	n/a	chr22:31885914-31885923 chr22:31886074-31886083 chr22:31885969-31885978 chr22:31886000-31886009
43	EBF1	chr22:31886421-31887000	GM12878	blood:	n/a	n/a
44	POLR2A	chr22:31884984-31887127	GM19193	blood:	n/a	n/a
45	POLR2A	chr22:31885744-31887162	GM12891	blood:	n/a	n/a
46	CEBPB	chr22:31885932-31887051	GM12878	blood:	n/a	chr22:31886493-31886501
47	POLR2A	chr22:31885106-31887465	GM12878	blood:	n/a	n/a
48	BCLAF1	chr22:31885626-31887091	GM12878	blood:	n/a	chr22:31885687-31885700 chr22:31886110-31886123 chr22:31885839-31885848 chr22:31885911-31885924 chr22:31885686-31885695 chr22:31886109-31886118 chr22:31886609-31886618
49	POLR2A	chr22:31885581-31887709	SK-N-MC	brain:	n/a	n/a
50	POLR2A	chr22:31885618-31887083	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:31884354..31887535-chr22:32340375..32343416,3	MCF-7	breast:
2	22:31864703-31891033..22:31936958-31958600	GM12878	blood:
3	chr22:31739041..31741328-chr22:31886288..31888294,2	MCF-7	breast:
4	chr22:31883675..31887496-chr22:32025240..32029301,5	K562	blood:
5	22:31864703-31891033..22:31930706-31935473	GM12878	blood:
6	22:31864703-31891033..22:32347255-32351014	K562	blood:
7	chr22:31876074..31877834-chr22:31886126..31888096,2	K562	blood:
8	chr22:31884997..31887735-chr22:32023066..32028730,7	MCF-7	breast:
9	chr22:31884998..31887254-chr22:32026687..32028800,2	K562	blood:
10	chr22:31793990..31796986-chr22:31884678..31887767,3	K562	blood:
11	chr22:31884599..31887538-chr22:32147471..32150641,3	K562	blood:
12	chr22:31884421..31887375-chr22:32024434..32026202,2	MCF-7	breast:
13	chr22:31793990..31795602-chr22:31885862..31887767,2	K562	blood:
14	chr22:31839629..31841921-chr22:31886106..31888362,2	K562	blood:
15	chr22:31741801..31743589-chr22:31885070..31888024,2	K562	blood:
16	chr22:31885118..31887084-chr22:32148124..32150324,2	MCF-7	breast:

Variant related genes	Relation type
EIF4ENIF1	TF binding region
ENSG00000128245	Chromatin interaction
ENSG00000213888	Chromatin interaction
ENSG00000214093	Chromatin interaction
ENSG00000128254	Chromatin interaction
ENSG00000100105	Chromatin interaction
ENSG00000229169	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000100150	Chromatin interaction
ENSG00000238910	Chromatin interaction
ENSG00000185721	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10483159	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs11089503	1.00[JPT][hapmap]
rs12169794	0.86[ASN][1000 genomes]
rs12484188	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12484233	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12484858	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12484966	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12485131	0.83[AMR][1000 genomes]
rs12485142	0.84[AMR][1000 genomes]
rs12485176	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17821048	1.00[JPT][hapmap]
rs17821132	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2273248	0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs2295240	0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs2295241	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413055	0.92[AMR][1000 genomes]
rs35047625	0.81[ASN][1000 genomes]
rs35208364	0.82[ASN][1000 genomes]
rs3747155	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[ASN][1000 genomes]
rs3788434	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs58055951	0.89[ASN][1000 genomes]
rs58915086	0.83[AMR][1000 genomes]
rs59416609	0.89[ASN][1000 genomes]
rs7287937	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs7293134	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9621263	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9621264	0.82[ASN][1000 genomes]
rs9621270	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

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	nsv1063634	chr22:31797004-31921254	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv459872	chr22:31833759-31977594	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
3	nsv588894	chr22:31833759-31977594	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1060776	chr22:31869892-31900359	Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3324564	chr22:31884577-31887325	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	esv3348685	chr22:31884652-31887150	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31884600-31887000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr22:31884600-31887000	Active TSS	Psoas Muscle	Psoas
3	chr22:31884600-31887000	Active TSS	Right Atrium	heart
4	chr22:31884600-31887200	Active TSS	Colonic Mucosa	Colon
5	chr22:31884600-31887200	Active TSS	Fetal Muscle Trunk	muscle
6	chr22:31884600-31887400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr22:31884800-31887000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr22:31884800-31887000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr22:31884800-31887000	Active TSS	Right Ventricle	heart
10	chr22:31884800-31887200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr22:31884800-31887200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr22:31884800-31887200	Active TSS	A549	lung
13	chr22:31884800-31887200	Active TSS	K562	blood
14	chr22:31885000-31887000	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr22:31885000-31887000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:31885000-31887000	Active TSS	Esophagus	oesophagus
17	chr22:31885000-31887000	Active TSS	Left Ventricle	heart
18	chr22:31885000-31887000	Active TSS	Lung	lung
19	chr22:31885200-31887000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr22:31885400-31887200	Active TSS	Thymus	Thymus
21	chr22:31886000-31887200	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr22:31886000-31887200	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr22:31886000-31887400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr22:31886000-31887600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr22:31886200-31887000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr22:31886200-31887200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr22:31886200-31887200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr22:31886200-31887200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr22:31886200-31887200	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr22:31886200-31887400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr22:31886200-31887400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr22:31886200-31887400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr22:31886200-31887400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr22:31886400-31887000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr22:31886400-31887000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr22:31886400-31887000	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr22:31886400-31887000	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr22:31886400-31887000	Active TSS	Placenta Amnion	Placenta Amnion
39	chr22:31886400-31887200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
40	chr22:31886400-31887200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr22:31886400-31887200	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr22:31886400-31887200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr22:31886400-31887200	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr22:31886400-31887200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr22:31886400-31887200	Flanking Active TSS	Fetal Thymus	thymus
46	chr22:31886400-31887200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr22:31886400-31887200	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr22:31886400-31887200	Flanking Active TSS	HUVEC	blood vessel
49	chr22:31886400-31887400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr22:31886400-31887400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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