Variant report

Variant	rs11119973
Chromosome Location	chr1:212734714-212734715
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	SMARCC1	chr1:212734593-212735201	Hela-S3	cervix:	n/a	n/a
2	SP1	chr1:212734245-212735489	HCT-116	colon:	n/a	n/a
3	POLR2A	chr1:212734692-212735299	HCT-116	colon:	n/a	n/a
4	GATA3	chr1:212734616-212735213	T-47D	breast:	n/a	n/a
5	JUND	chr1:212734696-212735334	Hela-S3	cervix:	n/a	chr1:212734742-212734754
6	CBX3	chr1:212734177-212735460	HCT-116	colon:	n/a	n/a
7	SPI1	chr1:212734423-212734752	GM12891	blood:	n/a	chr1:212734595-212734604 chr1:212734596-212734603 chr1:212734594-212734607 chr1:212734593-212734606
8	SPI1	chr1:212734411-212734737	GM12878	blood:	n/a	chr1:212734595-212734604 chr1:212734596-212734603 chr1:212734594-212734607 chr1:212734593-212734606
9	FOSL2	chr1:212734601-212735381	SK-N-SH	brain:	n/a	chr1:212734742-212734754
10	EP300	chr1:212734631-212735384	ECC-1	luminal epithelium:	n/a	chr1:212734735-212734742
11	TCF12	chr1:212734659-212735408	SK-N-SH	brain:	n/a	n/a
12	SPI1	chr1:212734369-212734732	GM12891	blood:	n/a	chr1:212734595-212734604 chr1:212734596-212734603 chr1:212734594-212734607 chr1:212734593-212734606
13	GTF2F1	chr1:212734650-212735216	Hela-S3	cervix:	n/a	n/a
14	FOSL1	chr1:212734611-212735454	HCT-116	colon:	n/a	chr1:212734742-212734754
15	FOSL1	chr1:212734484-212735554	HCT-116	colon:	n/a	chr1:212734742-212734754
16	JUND	chr1:212734595-212735499	HCT-116	colon:	n/a	chr1:212734742-212734754
17	TEAD4	chr1:212734674-212735426	ECC-1	luminal epithelium:	n/a	n/a
18	JUND	chr1:212734653-212735384	SK-N-SH	brain:	n/a	chr1:212734742-212734754
19	JUND	chr1:212734523-212735478	HCT-116	colon:	n/a	chr1:212734742-212734754

No.	Distal block	Cell Line	Cell type
1	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
2	chr1:212670746..212672683-chr1:212733125..212734851,2	K562	blood:
3	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:
4	chr1:212734422..212735324-chr2:162954257..162954966,2	HCT-116	colon:
5	chr1:212674417..212676345-chr1:212732607..212734870,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATF3-1	chr1:212734097-212734736	XLOC_000555

Variant related genes	Relation type
ATF3	TF binding region
ENSG00000162772	Chromatin interaction
ENSG00000264590	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10157292	0.92[ASN][1000 genomes]
rs10779581	1.00[ASW][hapmap];0.95[CHB][hapmap]
rs10863978	0.90[CHB][hapmap]
rs10863979	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10863980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10863981	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs1105899	0.83[CHD][hapmap];0.87[JPT][hapmap]
rs11119940	1.00[ASW][hapmap]
rs11119941	1.00[ASW][hapmap]
rs11119957	0.91[CHB][hapmap]
rs11119963	0.84[AMR][1000 genomes]
rs11119965	0.84[AMR][1000 genomes]
rs11119970	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11119971	1.00[ASW][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11119972	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11119974	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11119975	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11119977	1.00[JPT][hapmap]
rs11571528	0.83[LWK][hapmap]
rs12037048	0.93[ASN][1000 genomes]
rs12038766	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12041940	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12046640	0.93[ASN][1000 genomes]
rs12136405	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12729140	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1877474	0.93[JPT][hapmap]
rs3806460	0.95[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[ASN][1000 genomes]
rs4951447	1.00[ASW][hapmap]
rs4951448	1.00[ASW][hapmap]
rs4951453	0.86[AMR][1000 genomes]
rs4951606	0.85[CHB][hapmap]
rs4951609	0.95[CHB][hapmap];0.84[AMR][1000 genomes]
rs4951611	0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs4951613	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4951618	0.86[JPT][hapmap]
rs502502	0.84[JPT][hapmap]
rs606996	0.86[AMR][1000 genomes]
rs6674072	0.93[JPT][hapmap];1.00[LWK][hapmap]
rs678640	0.83[AMR][1000 genomes]
rs72649993	0.83[AMR][1000 genomes]
rs7553505	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs791561	0.86[AMR][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	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11119973	RNASE7	trans	parietal	SCAN
rs11119973	LOC642946	cis	multi-tissue	Pritchard

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212732400-212734800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:212732400-212734800	Weak transcription	Lung	lung
3	chr1:212732400-212734800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:212732400-212736000	Enhancers	Placenta	Placenta
5	chr1:212732800-212734800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:212732800-212734800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:212732800-212734800	Weak transcription	Left Ventricle	heart
8	chr1:212732800-212734800	Weak transcription	Right Atrium	heart
9	chr1:212732800-212735000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:212732800-212735000	Weak transcription	HMEC	breast
11	chr1:212732800-212738000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:212732800-212739600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:212732800-212739600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:212732800-212739800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:212732800-212739800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:212732800-212739800	Weak transcription	Stomach Mucosa	stomach
17	chr1:212732800-212740000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:212733000-212734800	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:212733000-212734800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:212733000-212735000	Weak transcription	NHEK	skin
21	chr1:212733000-212739600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:212733000-212739600	Weak transcription	Adipose Nuclei	Adipose
23	chr1:212733000-212739800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:212733000-212739800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:212733000-212740600	Weak transcription	Fetal Heart	heart
26	chr1:212733200-212739600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:212733400-212735000	Weak transcription	K562	blood
28	chr1:212733800-212735200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:212734000-212735000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:212734200-212734800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:212734200-212735000	Enhancers	NHDF-Ad	bronchial
32	chr1:212734200-212735400	Enhancers	HSMMtube	muscle
33	chr1:212734200-212735600	Enhancers	NH-A	brain
34	chr1:212734200-212736200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:212734400-212734800	Enhancers	Muscle Satellite Cultured Cells	--
36	chr1:212734400-212734800	Enhancers	HSMM	muscle
37	chr1:212734400-212734800	Enhancers	NHLF	lung
38	chr1:212734400-212734800	Enhancers	Osteobl	bone
39	chr1:212734400-212735200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr1:212734400-212735200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:212734400-212735200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr1:212734400-212735600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:212734400-212735600	Enhancers	HUVEC	blood vessel
44	chr1:212734400-212740000	Weak transcription	Aorta	Aorta
45	chr1:212734600-212734800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:212734600-212735200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:212734600-212735200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:212734600-212735200	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr1:212734600-212735200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr1:212734600-212735200	Flanking Active TSS	A549	lung

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