Variant report

Variant	rs4760611
Chromosome Location	chr12:48421449-48421450
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	FOXA1	chr12:48421398-48421827	HepG2	liver:	n/a	n/a
2	REST	chr12:48421118-48421492	PFSK-1	brain:	n/a	chr12:48421477-48421486

No.	Distal block	Cell Line	Cell type
1	chr12:48421385..48423662-chr12:48427630..48429692,2	K562	blood:
2	chr12:48420267..48422081-chr12:48425006..48427209,2	K562	blood:
3	chr12:48359708..48361971-chr12:48421078..48422974,2	MCF-7	breast:
4	chr12:48415815..48418237-chr12:48421031..48422834,2	K562	blood:

Variant related genes	Relation type
ENSG00000257955	TF binding region
ENSG00000134291	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1018973	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10492080	0.82[ASW][hapmap];0.86[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs10783226	0.83[EUR][1000 genomes]
rs10783227	0.87[EUR][1000 genomes]
rs10783231	0.90[GIH][hapmap];0.95[JPT][hapmap]
rs10783232	0.92[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs11168451	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs11168455	0.92[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs11609399	0.86[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs11612578	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11612970	0.89[EUR][1000 genomes]
rs11613485	0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs11613781	0.81[EUR][1000 genomes]
rs12580764	0.91[EUR][1000 genomes]
rs12581972	0.84[EUR][1000 genomes]
rs12822085	0.89[GIH][hapmap];0.95[JPT][hapmap]
rs1476608	0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs1635526	0.80[EUR][1000 genomes]
rs17122565	0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17122611	0.91[EUR][1000 genomes]
rs17122612	0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs17122613	0.90[EUR][1000 genomes]
rs17122651	0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs1793931	0.82[EUR][1000 genomes]
rs1793933	0.82[EUR][1000 genomes]
rs1859441	0.86[CEU][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs1859444	0.86[EUR][1000 genomes]
rs1968071	0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs1990029	0.91[EUR][1000 genomes]
rs2286022	0.91[EUR][1000 genomes]
rs3742074	0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs3803183	0.87[EUR][1000 genomes]
rs3803184	0.87[EUR][1000 genomes]
rs3825404	0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs4075913	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs4141065	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs4293182	0.90[EUR][1000 genomes]
rs4589362	0.86[EUR][1000 genomes]
rs4760614	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760615	0.95[EUR][1000 genomes]
rs4760618	0.92[EUR][1000 genomes]
rs4760620	0.82[ASW][hapmap];0.86[CEU][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap]
rs4760677	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760683	0.84[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs4760685	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs4760692	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs4760698	0.92[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs57054831	0.86[EUR][1000 genomes]
rs57380031	0.90[EUR][1000 genomes]
rs58046797	0.86[EUR][1000 genomes]
rs58331734	0.81[EUR][1000 genomes]
rs59766465	0.91[EUR][1000 genomes]
rs60567660	0.86[EUR][1000 genomes]
rs60629297	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60681522	0.91[EUR][1000 genomes]
rs6580647	0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs6580649	0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs6580651	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580656	0.89[JPT][hapmap]
rs6580660	0.95[JPT][hapmap]
rs7132668	0.90[EUR][1000 genomes]
rs7133249	0.91[EUR][1000 genomes]
rs726354	0.82[ASW][hapmap];0.86[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs72644841	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72644842	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72644843	0.91[EUR][1000 genomes]
rs72644844	0.91[EUR][1000 genomes]
rs72644845	0.81[EUR][1000 genomes]
rs7296913	0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs7305954	0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs7310579	0.95[EUR][1000 genomes]
rs7312326	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs7315258	0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs7485057	0.90[GIH][hapmap];0.95[JPT][hapmap]
rs757556	0.86[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs7957764	0.95[EUR][1000 genomes]
rs7959755	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7963934	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs7967762	0.80[CEU][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7969749	0.86[CEU][hapmap];0.95[JPT][hapmap]
rs7971668	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs879242	0.86[CEU][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs9651993	0.91[EUR][1000 genomes]
rs9805048	0.88[TSI][hapmap];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4760611	ASB8	cis	parietal	SCAN
rs4760611	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48416800-48423400	Weak transcription	Right Atrium	heart
2	chr12:48417800-48423400	Weak transcription	Fetal Lung	lung
3	chr12:48418000-48422200	Weak transcription	Fetal Heart	heart
4	chr12:48418200-48422200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr12:48418200-48424200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:48418400-48425800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:48418600-48425200	Enhancers	Fetal Intestine Large	intestine
8	chr12:48419200-48422400	Weak transcription	K562	blood
9	chr12:48420000-48422400	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:48420000-48424200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:48420200-48422800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:48420200-48423800	Enhancers	Primary hematopoietic stem cells	blood
13	chr12:48420200-48424200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:48420400-48421800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr12:48420400-48424000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:48420400-48424000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:48420400-48424200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:48420400-48429000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:48420600-48422200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:48420600-48424200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:48420800-48421600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:48420800-48421800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
23	chr12:48420800-48421800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr12:48420800-48421800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:48420800-48424600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:48421000-48421800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
27	chr12:48421000-48421800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:48421000-48421800	Flanking Active TSS	HepG2	liver
29	chr12:48421000-48422400	Weak transcription	Fetal Kidney	kidney
30	chr12:48421200-48421600	Enhancers	Duodenum Mucosa	Duodenum
31	chr12:48421400-48421800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
32	chr12:48421400-48421800	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr12:48421400-48421800	Enhancers	HMEC	breast
34	chr12:48421400-48422000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:48421400-48422800	Enhancers	Placenta Amnion	Placenta Amnion
36	chr12:48421400-48425000	Enhancers	Fetal Intestine Small	intestine

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