Variant report

Variant	rs9655049
Chromosome Location	chr7:5229600-5229601
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	POLR2A	chr7:5229553-5230133	GM12892	blood:	n/a	n/a
2	MXI1	chr7:5229583-5230487	GM12878	blood:	n/a	n/a
3	TBP	chr7:5229578-5229983	Hela-S3	cervix:	n/a	n/a
4	HA-E2F1	chr7:5229588-5230425	Hela-S3	cervix:	n/a	chr7:5229844-5229853 chr7:5229856-5229865
5	POLR2A	chr7:5229514-5229990	K562	blood:	n/a	n/a
6	IRF1	chr7:5229572-5230028	K562	blood:	n/a	chr7:5229843-5229857 chr7:5229793-5229807
7	SP1	chr7:5229544-5229998	GM12878	blood:	n/a	chr7:5229844-5229854 chr7:5229793-5229804 chr7:5229843-5229855 chr7:5229845-5229854 chr7:5229794-5229803 chr7:5229844-5229853 chr7:5229793-5229805 chr7:5229843-5229855 chr7:5229795-5229804 chr7:5229790-5229804 chr7:5229794-5229804 chr7:5229793-5229805 chr7:5229845-5229854 chr7:5229844-5229854
8	EGR1	chr7:5229563-5230018	MCF-7	breast:	n/a	chr7:5229838-5229853 chr7:5229839-5229852 chr7:5229840-5229854 chr7:5229839-5229853 chr7:5229842-5229851 chr7:5229844-5229854 chr7:5229839-5229852 chr7:5229840-5229851 chr7:5229839-5229852 chr7:5229842-5229852 chr7:5229839-5229852 chr7:5229841-5229851 chr7:5229789-5229802 chr7:5229790-5229804
9	RFX5	chr7:5229587-5230010	Hela-S3	cervix:	n/a	n/a
10	CREB1	chr7:5229522-5230082	K562	blood:	n/a	n/a
11	POLR2A	chr7:5229525-5230016	GM10847	blood:	n/a	n/a
12	POLR2A	chr7:5229374-5230194	PANC-1	pancreas:	n/a	n/a
13	NRF1	chr7:5229013-5230600	SK-N-SH	brain:	n/a	chr7:5229855-5229866 chr7:5229852-5229866 chr7:5229844-5229853 chr7:5229855-5229869 chr7:5229855-5229864 chr7:5229810-5229824
14	POLR2A	chr7:5229492-5230093	GM18526	blood:	n/a	n/a
15	KAP1	chr7:5229479-5229922	HEK293	kidney:	n/a	n/a
16	POLR2A	chr7:5229377-5230383	Hela-S3	cervix:	n/a	n/a
17	NRF1	chr7:5229542-5230052	H1-hESC	embryonic stem cell:	n/a	chr7:5229855-5229866 chr7:5229852-5229866 chr7:5229844-5229853 chr7:5229855-5229869 chr7:5229855-5229864 chr7:5229810-5229824
18	ZMIZ1	chr7:5229553-5230043	K562	blood:	n/a	n/a
19	POLR2A	chr7:5229411-5230153	Gliobla	brain:	n/a	n/a
20	POLR2A	chr7:5229472-5230032	U87	brain:	n/a	n/a
21	TAF1	chr7:5229483-5229981	PFSK-1	brain:	n/a	n/a
22	CEBPD	chr7:5229543-5230095	HepG2	liver:	n/a	n/a
23	CREB1	chr7:5229547-5230070	HepG2	liver:	n/a	n/a
24	MAZ	chr7:5229570-5230500	K562	blood:	n/a	chr7:5229794-5229804
25	GABPA	chr7:5229503-5229963	K562	blood:	n/a	chr7:5229855-5229866 chr7:5229852-5229866 chr7:5229844-5229853 chr7:5229855-5229869 chr7:5229855-5229864 chr7:5229810-5229824
26	ELF1	chr7:5229595-5229900	HepG2	liver:	n/a	chr7:5229842-5229854
27	POLR2A	chr7:5229504-5230041	H1-hESC	embryonic stem cell:	n/a	n/a
28	TAF1	chr7:5229551-5230356	HepG2	liver:	n/a	n/a
29	E2F6	chr7:5229596-5229933	A549	lung:	n/a	chr7:5229844-5229853 chr7:5229856-5229865
30	MTA3	chr7:5229522-5229817	GM12878	blood:	n/a	n/a
31	ELK1	chr7:5229582-5229924	Hela-S3	cervix:	n/a	n/a
32	ELF1	chr7:5229515-5230131	GM12878	blood:	n/a	chr7:5229842-5229854
33	E2F6	chr7:5229510-5229965	H1-hESC	embryonic stem cell:	n/a	chr7:5229844-5229853 chr7:5229856-5229865
34	HCFC1	chr7:5229560-5230060	K562	blood:	n/a	n/a
35	HEY1	chr7:5229543-5230044	HepG2	liver:	n/a	chr7:5229842-5229857 chr7:5229839-5229854 chr7:5229820-5229835
36	YY1	chr7:5229547-5230046	GM12878	blood:	n/a	chr7:5229844-5229853 chr7:5229850-5229861
37	FOXA1	chr7:5229552-5230004	HepG2	liver:	n/a	n/a
38	POLR2A	chr7:5229474-5230590	Hela-S3	cervix:	n/a	n/a
39	TRIM28	chr7:5229464-5229994	K562	blood:	n/a	n/a
40	POLR2A	chr7:5229020-5230440	HepG2	liver:	n/a	n/a
41	MAX	chr7:5229555-5230460	Hela-S3	cervix:	n/a	chr7:5229794-5229804
42	POLR2A	chr7:5229437-5230499	GM12878	blood:	n/a	n/a
43	PML	chr7:5229324-5229978	GM12878	blood:	n/a	n/a
44	MAX	chr7:5229543-5229990	K562	blood:	n/a	chr7:5229794-5229804
45	TEAD4	chr7:5229475-5229933	K562	blood:	n/a	n/a
46	SIN3AK20	chr7:5229453-5230546	PANC-1	pancreas:	n/a	n/a
47	MAX	chr7:5229416-5230145	HepG2	liver:	n/a	chr7:5229794-5229804
48	HEY1	chr7:5229520-5230117	K562	blood:	n/a	chr7:5229842-5229857 chr7:5229839-5229854 chr7:5229820-5229835
49	POLR2A	chr7:5229354-5230417	HUVEC	blood vessel:	n/a	n/a
50	YY1	chr7:5229592-5230268	K562	blood:	n/a	chr7:5229844-5229853 chr7:5229850-5229861

No.	Distal block	Cell Line	Cell type
1	chr10:70091732..70092683-chr7:5229307..5229918,2	NB4	blood:
2	chr7:5218548..5222992-chr7:5228147..5230588,3	MCF-7	breast:
3	chr1:11968100..11968787-chr7:5229394..5230254,2	Hela-S3	cervix:

Variant related genes	Relation type
WIPI2	TF binding region
ENSG00000202039	Chromatin interaction
ENSG00000096746	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000108187	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10951837	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11772474	0.83[ASN][1000 genomes]
rs12539634	0.82[ASN][1000 genomes]
rs4352737	0.91[ASN][1000 genomes]
rs4724449	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530968	chr7:4572250-5418004	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1031697	chr7:4677463-5241790	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer 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 miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv538704	chr7:4677463-5241790	Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
5	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
6	nsv1031007	chr7:5101766-5262695	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv916396	chr7:5128917-5370805	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
9	nsv1015639	chr7:5209510-5255399	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	nsv887390	chr7:5224407-5411296	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv887391	chr7:5224407-5572132	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	292 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:147 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5228800-5231000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr7:5229000-5229600	Flanking Active TSS	Dnd41	blood
3	chr7:5229200-5229600	Enhancers	Primary hematopoietic stem cells	blood
4	chr7:5229200-5229600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr7:5229200-5229600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr7:5229200-5229600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:5229200-5229600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
8	chr7:5229200-5229600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr7:5229200-5229600	Enhancers	Spleen	Spleen
10	chr7:5229200-5229800	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr7:5229200-5229800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr7:5229200-5230200	Active TSS	Stomach Smooth Muscle	stomach
13	chr7:5229200-5230400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:5229200-5230400	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr7:5229200-5230400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr7:5229200-5230400	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr7:5229200-5230400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:5229200-5230400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:5229200-5230400	Active TSS	Brain Cingulate Gyrus	brain
20	chr7:5229200-5230400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:5229200-5230400	Active TSS	Fetal Brain Female	brain
22	chr7:5229200-5230400	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr7:5229200-5230600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:5229200-5230600	Active TSS	Brain Hippocampus Middle	brain
25	chr7:5229200-5230800	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr7:5229200-5230800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr7:5229200-5230800	Active TSS	Brain Anterior Caudate	brain
28	chr7:5229200-5230800	Active TSS	Fetal Intestine Large	intestine
29	chr7:5229200-5231000	Active TSS	H1 Cell Line	embryonic stem cell
30	chr7:5229200-5231000	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr7:5229200-5231000	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr7:5229200-5231000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:5229200-5231000	Active TSS	Muscle Satellite Cultured Cells	--
34	chr7:5229200-5231000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr7:5229200-5231000	Active TSS	Stomach Mucosa	stomach
36	chr7:5229200-5231000	Active TSS	A549	lung
37	chr7:5229200-5231000	Active TSS	Hela-S3	cervix
38	chr7:5229200-5231400	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr7:5229200-5231400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr7:5229200-5231600	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr7:5229400-5229600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr7:5229400-5229600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr7:5229400-5229600	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr7:5229400-5229600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr7:5229400-5229600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr7:5229400-5229600	Flanking Active TSS	Liver	Liver
47	chr7:5229400-5229600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr7:5229400-5229600	Flanking Active TSS	Fetal Intestine Small	intestine
49	chr7:5229400-5229600	Flanking Active TSS	Fetal Muscle Trunk	muscle
50	chr7:5229400-5229600	Flanking Active TSS	Fetal Muscle Leg	muscle

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