Variant report

Variant	rs10779576
Chromosome Location	chr1:212408261-212408262
allele	C/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	chr1:212407879-212408349	K562	blood:	n/a	n/a
2	POLR2A	chr1:212407915-212408352	HCT-116	colon:	n/a	n/a
3	SP1	chr1:212407925-212408413	A549	lung:	n/a	n/a
4	STAT3	chr1:212408036-212408261	MCF10A-Er-Src	breast:	n/a	n/a
5	JUND	chr1:212407831-212408507	K562	blood:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408135-212408142 chr1:212408248-212408260 chr1:212408133-212408144
6	IRF1	chr1:212407849-212408338	K562	blood:	n/a	n/a
7	UBTF	chr1:212408053-212408298	K562	blood:	n/a	n/a
8	CBX3	chr1:212407794-212408522	HCT-116	colon:	n/a	chr1:212408291-212408302
9	MAZ	chr1:212407854-212408384	K562	blood:	n/a	n/a
10	FOSL1	chr1:212407675-212408517	HCT-116	colon:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408135-212408142 chr1:212408133-212408144 chr1:212408248-212408260
11	JUND	chr1:212407967-212408349	A549	lung:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408135-212408142 chr1:212408248-212408260 chr1:212408133-212408144
12	BCL11A	chr1:212407952-212408323	GM12878	blood:	n/a	n/a
13	JUND	chr1:212407544-212408570	SK-N-SH	brain:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408135-212408142 chr1:212408248-212408260 chr1:212408133-212408144
14	POLR2A	chr1:212407905-212408288	K562	blood:	n/a	n/a
15	SP1	chr1:212407632-212408711	HCT-116	colon:	n/a	n/a
16	ATF3	chr1:212407867-212408294	K562	blood:	n/a	n/a
17	TAF1	chr1:212407888-212408278	K562	blood:	n/a	n/a
18	FOS	chr1:212407919-212408484	MCF10A-Er-Src	breast:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408133-212408144 chr1:212408135-212408142 chr1:212408248-212408260
19	CBX3	chr1:212407596-212408515	HCT-116	colon:	n/a	chr1:212408291-212408302
20	REST	chr1:212407825-212408351	K562	blood:	n/a	n/a
21	JUND	chr1:212407923-212408291	A549	lung:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408135-212408142 chr1:212408248-212408260 chr1:212408133-212408144
22	FOSL2	chr1:212407933-212408417	HepG2	liver:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408135-212408142 chr1:212408248-212408260 chr1:212408134-212408145
23	STAT3	chr1:212407885-212408275	MCF10A-Er-Src	breast:	n/a	n/a
24	JUND	chr1:212407811-212408480	SK-N-SH	brain:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408135-212408142 chr1:212408248-212408260 chr1:212408133-212408144
25	BATF	chr1:212407972-212408315	GM12878	blood:	n/a	chr1:212408131-212408142
26	RAD21	chr1:212407965-212408270	SK-N-SH_RA	brain:	n/a	n/a
27	MEF2C	chr1:212407851-212408479	GM12878	blood:	n/a	chr1:212408181-212408196 chr1:212408183-212408197
28	FOS	chr1:212407871-212408352	K562	blood:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408133-212408144 chr1:212408135-212408142 chr1:212408248-212408260
29	JUN	chr1:212407421-212408656	K562	blood:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408135-212408142 chr1:212408248-212408260
30	TCF12	chr1:212407776-212408527	SK-N-SH	brain:	n/a	n/a
31	MAX	chr1:212407719-212408538	HCT-116	colon:	n/a	n/a
32	EP300	chr1:212408000-212408397	GM12878	blood:	n/a	chr1:212408357-212408371 chr1:212408135-212408144
33	JUN	chr1:212407934-212408349	K562	blood:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408135-212408142 chr1:212408248-212408260
34	FOS	chr1:212407967-212408323	Hela-S3	cervix:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408133-212408144 chr1:212408135-212408142 chr1:212408248-212408260
35	JUND	chr1:212407908-212408397	Hela-S3	cervix:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408135-212408142 chr1:212408248-212408260 chr1:212408133-212408144
36	SMARCC1	chr1:212407816-212408451	Hela-S3	cervix:	n/a	chr1:212408135-212408144
37	FOS	chr1:212407906-212408343	HUVEC	blood vessel:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408133-212408144 chr1:212408135-212408142 chr1:212408248-212408260
38	TEAD4	chr1:212407659-212408661	K562	blood:	n/a	chr1:212408380-212408389
39	MEF2A	chr1:212407766-212408488	SK-N-SH	brain:	n/a	chr1:212408182-212408197 chr1:212408183-212408197
40	SP1	chr1:212407653-212408665	HCT-116	colon:	n/a	n/a
41	MAFK	chr1:212407729-212408361	K562	blood:	n/a	chr1:212408135-212408145
42	MEF2A	chr1:212407883-212408408	K562	blood:	n/a	chr1:212408182-212408197 chr1:212408183-212408197
43	FOS	chr1:212407931-212408359	MCF10A-Er-Src	breast:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408133-212408144 chr1:212408135-212408142 chr1:212408248-212408260
44	ZC3H11A	chr1:212407643-212408396	K562	blood:	n/a	n/a
45	JUN	chr1:212407957-212408338	HUVEC	blood vessel:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408135-212408142 chr1:212408248-212408260
46	RFX5	chr1:212407972-212408341	Hela-S3	cervix:	n/a	n/a
47	ATF2	chr1:212407886-212408401	GM12878	blood:	n/a	n/a
48	FOS	chr1:212407926-212408575	MCF10A-Er-Src	breast:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408133-212408144 chr1:212408135-212408142 chr1:212408248-212408260
49	FOSL2	chr1:212407928-212408287	A549	lung:	n/a	chr1:212408135-212408144 chr1:212408138-212408146 chr1:212408135-212408142 chr1:212408248-212408260 chr1:212408134-212408145
50	BCLAF1	chr1:212407879-212408345	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000226251	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11119881	0.85[ASN][1000 genomes]
rs1472225	0.87[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1873298	0.85[ASN][1000 genomes]
rs1962127	0.82[ASN][1000 genomes]
rs1967115	0.85[ASN][1000 genomes]
rs2921128	0.82[CHB][hapmap]
rs4951578	0.85[ASN][1000 genomes]
rs4951584	0.87[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7548606	0.86[ASN][1000 genomes]
rs792433	0.82[CHB][hapmap]
rs792443	0.82[CHB][hapmap]
rs903123	0.82[AMR][1000 genomes];0.90[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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	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
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10779576	LOC148696	cis	parietal	SCAN
rs10779576	IL24	cis	cerebellum	SCAN
rs10779576	VASH2	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212401400-212408400	Weak transcription	Lung	lung
2	chr1:212401800-212409000	Weak transcription	Gastric	stomach
3	chr1:212403400-212409000	Weak transcription	Fetal Intestine Large	intestine
4	chr1:212403600-212409600	Weak transcription	Liver	Liver
5	chr1:212404800-212410800	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr1:212405200-212408800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:212405200-212410600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:212405600-212408600	Weak transcription	Pancreas	Pancrea
9	chr1:212405600-212409000	Weak transcription	Esophagus	oesophagus
10	chr1:212405600-212414800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:212405600-212416400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:212406400-212411000	Enhancers	HSMMtube	muscle
13	chr1:212406600-212409200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:212406600-212410800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:212406800-212408600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:212406800-212408600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:212406800-212408800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:212406800-212409800	Enhancers	Fetal Muscle Leg	muscle
19	chr1:212406800-212410400	Enhancers	HSMM	muscle
20	chr1:212406800-212410600	Enhancers	Stomach Mucosa	stomach
21	chr1:212407000-212409200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:212407200-212410400	Enhancers	Left Ventricle	heart
23	chr1:212407400-212408600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:212407400-212408600	Enhancers	GM12878-XiMat	blood
25	chr1:212407400-212408800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:212407600-212408400	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr1:212407600-212408600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:212407600-212408600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:212407600-212408600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:212407600-212408600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:212407600-212408600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr1:212407600-212408600	Enhancers	Adipose Nuclei	Adipose
33	chr1:212407600-212408600	Enhancers	Colon Smooth Muscle	Colon
34	chr1:212407600-212408600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr1:212407600-212408600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr1:212407600-212408600	Enhancers	Psoas Muscle	Psoas
37	chr1:212407600-212408600	Enhancers	Rectal Smooth Muscle	rectum
38	chr1:212407600-212408600	Enhancers	Spleen	Spleen
39	chr1:212407600-212408600	Enhancers	A549	lung
40	chr1:212407600-212408600	Enhancers	HepG2	liver
41	chr1:212407600-212408600	Enhancers	HMEC	breast
42	chr1:212407600-212408600	Enhancers	HUVEC	blood vessel
43	chr1:212407600-212408600	Flanking Active TSS	K562	blood
44	chr1:212407600-212408600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr1:212407600-212408600	Enhancers	NH-A	brain
46	chr1:212407600-212408600	Enhancers	NHDF-Ad	bronchial
47	chr1:212407600-212408800	Enhancers	Hela-S3	cervix
48	chr1:212407600-212408800	Enhancers	NHEK	skin
49	chr1:212407600-212409200	Enhancers	NHLF	lung
50	chr1:212407600-212410000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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