Variant report

Variant	rs7485057
Chromosome Location	chr12:48578809-48578810
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	TAF1	chr12:48578529-48579776	H1-neurons	neurons:	n/a	n/a
2	SIN3A	chr12:48576618-48579251	H1-hESC	embryonic stem cell:	n/a	chr12:48577451-48577460
3	REST	chr12:48578514-48579455	H1-neurons	neurons:	n/a	n/a
4	MXI1	chr12:48576436-48579525	SK-N-SH	brain:	n/a	chr12:48577343-48577358 chr12:48577345-48577360 chr12:48577379-48577394 chr12:48577381-48577396
5	REST	chr12:48576228-48580563	H1-neurons	neurons:	n/a	chr12:48577348-48577357 chr12:48576911-48576924
6	MAX	chr12:48577849-48578831	H1-hESC	embryonic stem cell:	n/a	n/a
7	TAF1	chr12:48578404-48579318	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr12:48576694-48580496	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr12:48578332-48580491	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48578276..48580987-chr12:48583534..48585807,2	K562	blood:
2	chr12:48548408..48551386-chr12:48576630..48579457,3	K562	blood:
3	chr12:48576960..48580173-chr12:48592129..48594089,3	MCF-7	breast:
4	chr12:48549998..48552316-chr12:48577251..48580205,2	MCF-7	breast:
5	chr12:48577879..48579746-chr12:48586715..48588244,2	K562	blood:

Variant related genes	Relation type
ASB8	TF binding region
ENSG00000177981	Chromatin interaction
ENSG00000269514	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1018973	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs10492080	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1074174	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10783231	0.94[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783232	0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10783233	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11168449	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168451	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11168455	0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11609399	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11612578	0.95[JPT][hapmap]
rs11613485	0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs11613781	0.82[ASN][1000 genomes]
rs12822085	0.88[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1476608	0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs1489111	0.86[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]
rs17122565	0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs17122612	0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs17122651	0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs1968071	0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs2054902	0.81[JPT][hapmap]
rs2258342	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs2409001	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2634679	0.81[JPT][hapmap]
rs2634685	0.87[CEU][hapmap];0.83[MEX][hapmap]
rs2634699	0.86[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs2732455	0.80[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs2732458	0.82[MEX][hapmap]
rs2732477	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2732487	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs2932091	0.87[CEU][hapmap]
rs3742074	0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs4075913	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4141065	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4760611	0.90[GIH][hapmap];0.95[JPT][hapmap]
rs4760620	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4760683	0.86[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs4760685	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs4760692	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4760698	0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs57655233	0.82[ASN][1000 genomes]
rs58331734	0.82[ASN][1000 genomes]
rs6580653	0.91[ASN][1000 genomes]
rs6580656	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6580657	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6580660	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs726354	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs72644845	0.81[ASN][1000 genomes]
rs72644846	0.81[ASN][1000 genomes]
rs7296913	0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs7305418	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7312326	1.00[JPT][hapmap]
rs7313023	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7315258	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7485824	0.91[ASN][1000 genomes]
rs757556	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7963934	1.00[JPT][hapmap]
rs7969749	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7971668	1.00[JPT][hapmap]
rs879242	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs901962	0.81[JPT][hapmap]
rs901963	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs901964	0.86[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap]

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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7485057	ZNF641	cis	multi-tissue	Pritchard
rs7485057	MLL2	cis	cerebellum	SCAN
rs7485057	ZNF641	cis	Muscle Skeletal	GTEx
rs7485057	ASB8	cis	cerebellum	SCAN
rs7485057	ZNF641	cis	Whole Blood	GTEx
rs7485057	ASB8	cis	parietal	SCAN
rs7485057	H1T2	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48576200-48579000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:48576200-48579000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr12:48576600-48579000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr12:48576600-48579000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:48576600-48579000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
6	chr12:48576600-48580400	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr12:48576800-48580000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:48577200-48579000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:48577400-48579000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:48577800-48579000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:48577800-48579000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:48577800-48579000	Bivalent Enhancer	Fetal Thymus	thymus
13	chr12:48577800-48579200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
14	chr12:48578000-48579200	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr12:48578000-48579400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
16	chr12:48578000-48580000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr12:48578000-48580400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:48578200-48579000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr12:48578200-48580400	Enhancers	Esophagus	oesophagus
20	chr12:48578400-48579000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
21	chr12:48578400-48579200	Bivalent Enhancer	Primary B cells from cord blood	blood
22	chr12:48578400-48579400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:48578400-48579600	Active TSS	Brain Hippocampus Middle	brain
24	chr12:48578400-48580000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:48578400-48580400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:48578600-48579000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
27	chr12:48578600-48579000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
28	chr12:48578600-48579000	Enhancers	Brain Substantia Nigra	brain
29	chr12:48578600-48579000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
30	chr12:48578600-48579200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:48578600-48579200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:48578600-48579200	Bivalent/Poised TSS	Fetal Brain Female	brain
33	chr12:48578600-48579400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
34	chr12:48578600-48579600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:48578600-48579800	Active TSS	Fetal Brain Male	brain
36	chr12:48578600-48580000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:48578600-48580200	Active TSS	Brain Angular Gyrus	brain
38	chr12:48578600-48580400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:48578800-48579000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
40	chr12:48578800-48579000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:48578800-48579000	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr12:48578800-48579200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
43	chr12:48578800-48579200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
44	chr12:48578800-48579400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:48578800-48579400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr12:48578800-48579600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:48578800-48579600	Enhancers	Primary B cells from peripheral blood	blood
48	chr12:48578800-48579600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr12:48578800-48579600	Bivalent/Poised TSS	Placenta	Placenta
50	chr12:48578800-48579800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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