Variant report

Variant	rs7486941
Chromosome Location	chr12:48578631-48578632
allele	C/G/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	MAX	chr12:48577897-48578780	H1-hESC	embryonic stem cell:	n/a	n/a
5	MXI1	chr12:48576436-48579525	SK-N-SH	brain:	n/a	chr12:48577343-48577358 chr12:48577345-48577360 chr12:48577379-48577394 chr12:48577381-48577396
6	REST	chr12:48576228-48580563	H1-neurons	neurons:	n/a	chr12:48577348-48577357 chr12:48576911-48576924
7	MAX	chr12:48577849-48578831	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F6	chr12:48577847-48578788	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF1	chr12:48578404-48579318	H1-neurons	neurons:	n/a	n/a
10	CTCF	chr12:48578560-48578710	GM12872	blood:	n/a	n/a
11	CTBP2	chr12:48576803-48578719	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr12:48576694-48580496	H1-neurons	neurons:	n/a	n/a
13	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: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10875718	0.83[GIH][hapmap]
rs10875719	0.88[GIH][hapmap]
rs10875743	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs10875749	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs10875753	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs10875763	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107654	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs11168408	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11168428	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs11168437	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap]
rs11168441	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs11168460	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11168464	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11168468	0.83[ASN][1000 genomes]
rs11168474	0.83[ASN][1000 genomes]
rs11168484	0.83[ASN][1000 genomes]
rs12228750	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs12368659	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs12816820	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes]
rs12828309	0.83[ASN][1000 genomes]
rs12829841	0.83[ASN][1000 genomes]
rs1476607	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs1542707	0.83[ASN][1000 genomes]
rs1552550	0.83[ASN][1000 genomes]
rs2051851	0.81[CEU][hapmap]
rs2054905	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2408955	0.82[GIH][hapmap]
rs2450994	1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap]
rs2468943	0.81[GIH][hapmap]
rs2634681	1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap]
rs2634684	1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap]
rs2634697	0.83[ASN][1000 genomes]
rs2732445	0.83[ASN][1000 genomes]
rs2732448	1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap]
rs2732457	1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap]
rs2732466	1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap]
rs2732480	0.83[GIH][hapmap]
rs2732481	1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap]
rs2732484	1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap]
rs2956710	0.83[ASN][1000 genomes]
rs3087716	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34286639	0.83[ASN][1000 genomes]
rs3997	0.81[CEU][hapmap]
rs4760612	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4760679	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs6580650	0.81[CEU][hapmap];0.90[GIH][hapmap]
rs6580654	0.80[AMR][1000 genomes]
rs6580662	0.83[ASN][1000 genomes]
rs7139330	1.00[CHB][hapmap]
rs7297824	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7301003	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs7307566	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7315820	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7487682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7966829	0.83[ASN][1000 genomes]
rs7975632	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap]
rs8716	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]
rs923397	1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap]
rs973398	0.81[CEU][hapmap];1.00[CHB][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7486941	TMEM131	trans	parietal	SCAN
rs7486941	H1FNT	cis	Muscle Skeletal	GTEx
rs7486941	DDX23	cis	parietal	SCAN
rs7486941	ZNF641	cis	cerebellum	SCAN

Chromatin state (count:67 , 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	chr12:48576400-48578800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:48576400-48578800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
5	chr12:48576600-48578800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
6	chr12:48576600-48579000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr12:48576600-48579000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:48576600-48579000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
9	chr12:48576600-48580400	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr12:48576800-48578800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr12:48576800-48580000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:48577200-48578800	Active TSS	Ovary	ovary
13	chr12:48577200-48579000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:48577400-48578800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:48577400-48578800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:48577400-48578800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:48577400-48578800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
18	chr12:48577400-48579000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:48577600-48578800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:48577600-48578800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
21	chr12:48577800-48578800	Bivalent/Poised TSS	Adipose Nuclei	Adipose
22	chr12:48577800-48578800	Bivalent/Poised TSS	NH-A	brain
23	chr12:48577800-48579000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:48577800-48579000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:48577800-48579000	Bivalent Enhancer	Fetal Thymus	thymus
26	chr12:48577800-48579200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
27	chr12:48578000-48578800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr12:48578000-48578800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:48578000-48578800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr12:48578000-48579200	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr12:48578000-48579400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
32	chr12:48578000-48580000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr12:48578000-48580400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:48578200-48578800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:48578200-48578800	Enhancers	Spleen	Spleen
36	chr12:48578200-48578800	Flanking Bivalent TSS/Enh	NHEK	skin
37	chr12:48578200-48579000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr12:48578200-48580400	Enhancers	Esophagus	oesophagus
39	chr12:48578400-48578800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr12:48578400-48578800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
41	chr12:48578400-48578800	Flanking Bivalent TSS/Enh	Placenta	Placenta
42	chr12:48578400-48579000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
43	chr12:48578400-48579200	Bivalent Enhancer	Primary B cells from cord blood	blood
44	chr12:48578400-48579400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:48578400-48579600	Active TSS	Brain Hippocampus Middle	brain
46	chr12:48578400-48580000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:48578400-48580400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:48578600-48578800	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr12:48578600-48578800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr12:48578600-48578800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--

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