Variant report

Variant	rs542278
Chromosome Location	chr12:57872720-57872721
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	RCOR1	chr12:57872719-57873889	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:57870713-57874109	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:57871720-57874107	GM12892	blood:	n/a	n/a
4	POLR2A	chr12:57870698-57874248	GM12892	blood:	n/a	n/a
5	MTA3	chr12:57869729-57872927	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:57870841-57874110	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57871859..57875002-chr12:57911901..57914526,3	K562	blood:
2	chr12:57870756..57873648-chr12:57892885..57895299,2	K562	blood:
3	chr12:57871719..57874359-chr12:57913952..57915597,2	MCF-7	breast:
4	chr12:57641973..57643860-chr12:57871922..57873814,2	K562	blood:

Variant related genes	Relation type
ARHGAP9	TF binding region
ENSG00000166987	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000185482	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1148554	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1148555	0.91[ASW][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs1148556	0.85[MKK][hapmap]
rs1148557	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap]
rs1284465	0.84[AMR][1000 genomes]
rs1284605	0.84[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs1284606	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1299737	0.82[AMR][1000 genomes]
rs1617196	0.92[EUR][1000 genomes]
rs1629410	0.82[AMR][1000 genomes]
rs1669296	0.84[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs1678537	0.91[ASW][hapmap];0.83[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs1709871	0.83[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs1709874	0.80[AMR][1000 genomes]
rs2127318	0.86[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap]
rs2620677	0.81[AMR][1000 genomes]
rs2620679	0.91[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs2672571	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2943696	0.86[AMR][1000 genomes]
rs3847699	0.86[CHB][hapmap]
rs472895	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474544	0.84[AMR][1000 genomes]
rs496245	0.83[CEU][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes]
rs508904	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs511752	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539244	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541869	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs569251	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs697221	0.84[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs703835	0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs703837	0.86[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs747340	0.82[AMR][1000 genomes]
rs775241	0.86[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs775324	0.91[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs776038	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs776039	0.80[AMR][1000 genomes]
rs7964074	0.91[GIH][hapmap];0.96[TSI][hapmap]
rs796546	0.82[AMR][1000 genomes]
rs899653	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9737891	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs542278	ACVRL1	cis	cerebellum	SCAN
rs542278	ITGB7	cis	cerebellum	SCAN
rs542278	KRT81	cis	parietal	SCAN
rs542278	AVIL	cis	cerebellum	SCAN
rs542278	CALCOCO1	cis	cerebellum	SCAN
rs542278	STAT6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57869200-57874200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr12:57869200-57874800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:57869400-57874000	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr12:57869400-57874000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:57869400-57874200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr12:57869600-57874000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr12:57869600-57874400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr12:57869800-57873600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:57869800-57874000	Flanking Active TSS	Primary B cells from peripheral blood	blood
10	chr12:57870200-57873200	Active TSS	Liver	Liver
11	chr12:57870200-57874200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:57870400-57874000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr12:57870600-57873400	Active TSS	Esophagus	oesophagus
14	chr12:57870800-57873200	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr12:57870800-57873600	Enhancers	K562	blood
16	chr12:57871000-57874000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:57871000-57874000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr12:57871200-57873600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:57871200-57873600	Active TSS	Rectal Smooth Muscle	rectum
20	chr12:57871400-57872800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:57871400-57873200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:57871400-57873600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:57871600-57872800	Weak transcription	Lung	lung
24	chr12:57871600-57873000	Active TSS	Colonic Mucosa	Colon
25	chr12:57871600-57873600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr12:57871600-57873600	Enhancers	Spleen	Spleen
27	chr12:57871600-57881200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:57871600-57881200	Weak transcription	Right Atrium	heart
29	chr12:57871800-57873800	Flanking Active TSS	GM12878-XiMat	blood
30	chr12:57871800-57874000	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr12:57871800-57874000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:57871800-57874000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr12:57871800-57875000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr12:57871800-57875000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr12:57871800-57875000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr12:57872000-57873200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:57872000-57873400	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr12:57872000-57874000	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
39	chr12:57872000-57874800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr12:57872000-57874800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr12:57872000-57877000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr12:57872400-57872800	Active TSS	Brain Substantia Nigra	brain
43	chr12:57872400-57872800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
44	chr12:57872400-57872800	Enhancers	Thymus	Thymus
45	chr12:57872400-57873000	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr12:57872400-57873200	Bivalent Enhancer	Fetal Muscle Leg	muscle
47	chr12:57872400-57873400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:57872400-57873400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr12:57872400-57873600	Enhancers	HSMM	muscle
50	chr12:57872400-57875800	Enhancers	Fetal Thymus	thymus

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