Variant report

Variant	rs2303922
Chromosome Location	chr7:150725722-150725723
allele	A/C
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	FOS	chr7:150725208-150726113	MCF10A-Er-Src	breast:	n/a	n/a
2	ZNF263	chr7:150725189-150726000	K562	blood:	n/a	n/a
3	POLR2A	chr7:150725288-150726130	HepG2	liver:	n/a	n/a
4	ARID3A	chr7:150725605-150726124	HepG2	liver:	n/a	n/a
5	ELF1	chr7:150724932-150726082	MCF-7	breast:	n/a	n/a
6	RAD21	chr7:150725596-150726132	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr7:150724914-150726283	SK-N-SH	brain:	n/a	chr7:150725376-150725386
8	MAX	chr7:150724890-150726387	HCT-116	colon:	n/a	n/a
9	EP300	chr7:150725027-150726209	ECC-1	luminal epithelium:	n/a	chr7:150725353-150725362 chr7:150725368-150725384
10	NRF1	chr7:150725630-150725914	H1-hESC	embryonic stem cell:	n/a	chr7:150725778-150725789
11	HMGN3	chr7:150725213-150726080	K562	blood:	n/a	n/a
12	POLR2A	chr7:150724969-150726104	K562	blood:	n/a	n/a
13	TBL1XR1	chr7:150725073-150726134	K562	blood:	n/a	n/a
14	RUNX3	chr7:150725011-150726099	GM12878	blood:	n/a	n/a
15	CTCF	chr7:150725710-150725982	GM10248	blood:	n/a	n/a
16	HDAC2	chr7:150725584-150726087	MCF-7	breast:	n/a	n/a
17	SP2	chr7:150725139-150725724	H1-hESC	embryonic stem cell:	n/a	chr7:150725466-150725489 chr7:150725516-150725531
18	GTF2F1	chr7:150725227-150726029	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr7:150725707-150725974	GM10266	blood:	n/a	n/a
20	POLR2A	chr7:150725435-150725863	A549	lung:	n/a	n/a
21	NFYB	chr7:150725036-150725965	Hela-S3	cervix:	n/a	chr7:150725482-150725492 chr7:150725439-150725454 chr7:150725477-150725492
22	POLR2A	chr7:150725189-150726369	GM12878	blood:	n/a	n/a
23	CTCF	chr7:150725372-150726075	GM12878	blood:	n/a	chr7:150725376-150725386
24	CREB1	chr7:150725073-150726017	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr7:150725042-150726129	GM12892	blood:	n/a	n/a
26	MYC	chr7:150725056-150726155	K562	blood:	n/a	n/a
27	MAFK	chr7:150725339-150725939	HepG2	liver:	n/a	n/a
28	POLR2A	chr7:150725041-150725909	PANC-1	pancreas:	n/a	n/a
29	SMC3	chr7:150725145-150726105	Hela-S3	cervix:	n/a	chr7:150725377-150725387
30	RCOR1	chr7:150725108-150726066	GM12878	blood:	n/a	n/a
31	IRF1	chr7:150723712-150726126	K562	blood:	n/a	chr7:150725350-150725359
32	RAD21	chr7:150725502-150726106	IMR90	lung:	n/a	n/a
33	SP1	chr7:150724980-150726134	A549	lung:	n/a	chr7:150725520-150725531 chr7:150725379-150725391 chr7:150725379-150725391 chr7:150725380-150725389
34	SIN3AK20	chr7:150725038-150726129	SK-N-SH	brain:	n/a	n/a
35	THAP1	chr7:150725137-150725968	K562	blood:	n/a	n/a
36	RCOR1	chr7:150723966-150726437	K562	blood:	n/a	n/a
37	CTCF	chr7:150725707-150725996	NHEK	skin:	n/a	n/a
38	TAF1	chr7:150725606-150726043	GM12878	blood:	n/a	n/a
39	NFYA	chr7:150725096-150726053	K562	blood:	n/a	chr7:150725482-150725492
40	USF1	chr7:150724882-150725993	SK-N-SH	brain:	n/a	chr7:150725052-150725063
41	CTCF	chr7:150725672-150725972	GM13977	blood:	n/a	n/a
42	E2F4	chr7:150725330-150725934	GM12878	blood:	n/a	chr7:150725380-150725389
43	MYC	chr7:150723630-150726253	K562	blood:	n/a	n/a
44	YY1	chr7:150724979-150726014	K562	blood:	n/a	n/a
45	SP2	chr7:150725095-150725941	HepG2	liver:	n/a	chr7:150725466-150725489 chr7:150725516-150725531
46	MAX	chr7:150725041-150726056	Hela-S3	cervix:	n/a	n/a
47	EBF1	chr7:150725183-150725917	GM12878	blood:	n/a	n/a
48	SIX5	chr7:150725302-150725983	GM12878	blood:	n/a	n/a
49	MXI1	chr7:150725076-150726093	GM12878	blood:	n/a	n/a
50	TCF12	chr7:150725701-150726000	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:150718943..150723286-chr7:150723746..150726907,4	MCF-7	breast:
2	chr7:150725287..150725963-chr7:150753231..150754053,3	K562	blood:
3	chr7:150725439..150727092-chr7:150922758..150925738,2	K562	blood:
4	chr7:150725331..150726357-chr7:150756071..150757624,5	K562	blood:
5	chr7:150725480..150725995-chr7:150756426..150757309,2	MCF-7	breast:
6	chr1:11967969..11968473-chr7:150725442..150726079,2	Hela-S3	cervix:
7	chr7:150712297..150714427-chr7:150725298..150727101,2	MCF-7	breast:
8	chr7:150719730..150723078-chr7:150724265..150726856,4	MCF-7	breast:
9	chr15:65596970..65597811-chr7:150725386..150725988,2	Hela-S3	cervix:
10	chr7:150687026..150688559-chr7:150724058..150726072,2	MCF-7	breast:
11	chr7:150725482..150726344-chr7:150756570..150757185,2	MCF-7	breast:
12	chr7:150705481..150706887-chr7:150725454..150726471,3	K562	blood:
13	chr7:150725565..150726404-chr7:150753483..150754857,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NOS3-1	chr7:150725524-150725939	NONHSAT124169
2	lnc-NOS3-1	chr7:150725563-150726074	NONHSAT124175

Variant related genes	Relation type
ATG9B	TF binding region
ABCB8	TF binding region
ENSG00000200156	Chromatin interaction
ENSG00000164867	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000181652	Chromatin interaction
ENSG00000164885	Chromatin interaction
ENSG00000164889	Chromatin interaction
ENSG00000033050	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12539332	0.83[ASN][1000 genomes]
rs2116023	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303924	0.94[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2303926	0.93[ASN][1000 genomes]
rs2373927	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35900662	0.93[ASN][1000 genomes]
rs4148848	0.94[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs61218626	0.86[ASN][1000 genomes]
rs6944859	0.92[ASN][1000 genomes]
rs6944935	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6947821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821419	chr7:150593315-150974269	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
2	nsv1022246	chr7:150619660-150779924	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv889465	chr7:150640285-150800823	Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1017863	chr7:150643928-150779924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv539197	chr7:150643928-150779924	Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
6	nsv1028645	chr7:150643928-150806534	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv539198	chr7:150643928-150879259	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
8	nsv889469	chr7:150657209-150747746	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv889471	chr7:150700946-150751590	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv526410	chr7:150714812-150775306	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2303922	C7orf33	cis	parietal	SCAN
rs2303922	ABCB8	cis	cerebellum	SCAN
rs2303922	ATG9B	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150724000-150726600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:150724200-150726600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr7:150724400-150726400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr7:150724400-150726400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr7:150724600-150725800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:150724600-150725800	Bivalent/Poised TSS	HepG2	liver
7	chr7:150724600-150726400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr7:150724600-150726400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr7:150724800-150726000	Active TSS	Brain Hippocampus Middle	brain
10	chr7:150724800-150726000	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr7:150724800-150726000	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr7:150724800-150726200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:150724800-150726200	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr7:150724800-150726200	Active TSS	Brain Cingulate Gyrus	brain
15	chr7:150724800-150726200	Active TSS	Brain Substantia Nigra	brain
16	chr7:150724800-150726200	Active TSS	Fetal Kidney	kidney
17	chr7:150724800-150726400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr7:150724800-150726400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr7:150724800-150726400	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr7:150724800-150726400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:150724800-150726400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr7:150724800-150726400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr7:150724800-150726400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr7:150724800-150726400	Active TSS	Fetal Brain Female	brain
25	chr7:150724800-150726400	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr7:150724800-150726400	Active TSS	HSMMtube	muscle
27	chr7:150724800-150726400	Active TSS	NHLF	lung
28	chr7:150724800-150726600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:150724800-150726600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:150724800-150726600	Active TSS	Brain Angular Gyrus	brain
31	chr7:150724800-150726600	Active TSS	Rectal Smooth Muscle	rectum
32	chr7:150724800-150726600	Active TSS	NHDF-Ad	bronchial
33	chr7:150724800-150726800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr7:150725000-150726000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:150725000-150726000	Active TSS	Colonic Mucosa	Colon
36	chr7:150725000-150726000	Active TSS	Fetal Intestine Large	intestine
37	chr7:150725000-150726000	Active TSS	Pancreas	Pancrea
38	chr7:150725000-150726000	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr7:150725000-150726000	Active TSS	Stomach Smooth Muscle	stomach
40	chr7:150725000-150726000	Active TSS	Thymus	Thymus
41	chr7:150725000-150726200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr7:150725000-150726200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr7:150725000-150726200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:150725000-150726200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:150725000-150726200	Active TSS	Aorta	Aorta
46	chr7:150725000-150726200	Active TSS	Colon Smooth Muscle	Colon
47	chr7:150725000-150726200	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr7:150725000-150726200	Active TSS	Esophagus	oesophagus
49	chr7:150725000-150726200	Active TSS	Left Ventricle	heart
50	chr7:150725000-150726200	Active TSS	Lung	lung

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