Variant report

Variant	rs7103648
Chromosome Location	chr11:47461783-47461784
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr11:47461602-47461997	HepG2	liver:	n/a	n/a
2	HDAC2	chr11:47461586-47461977	HepG2	liver:	n/a	n/a
3	FOXA1	chr11:47461643-47461986	HepG2	liver:	n/a	n/a
4	SP1	chr11:47461566-47462055	HepG2	liver:	n/a	n/a
5	MYBL2	chr11:47461454-47461911	HepG2	liver:	n/a	n/a
6	EP300	chr11:47461561-47462003	HepG2	liver:	n/a	n/a
7	HNF4G	chr11:47461635-47461955	HepG2	liver:	n/a	n/a
8	RCOR1	chr11:47461584-47461937	HepG2	liver:	n/a	n/a
9	ZNF143	chr11:47461653-47461817	K562	blood:	n/a	n/a
10	ELF1	chr11:47461592-47461818	HepG2	liver:	n/a	n/a
11	RCOR1	chr11:47461781-47461836	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47461517..47464157-chr11:47469005..47471095,2	K562	blood:
2	chr11:47461517..47466481-chr11:47469061..47471319,5	K562	blood:
3	chr11:47446295..47450524-chr11:47461441..47464685,6	MCF-7	breast:

No data

Variant related genes	Relation type
RNU6-1302P	TF binding region
ENSG00000165916	Chromatin interaction
ENSG00000165917	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10437655	0.83[EUR][1000 genomes]
rs10742802	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10742814	0.95[JPT][hapmap]
rs10769263	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10769264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838702	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10838705	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838725	0.82[ASN][1000 genomes]
rs10838726	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10838732	0.95[JPT][hapmap]
rs11039221	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039244	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11039280	1.00[JPT][hapmap]
rs11606287	0.91[CEU][hapmap]
rs12292911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12361415	0.82[CHB][hapmap]
rs12577643	0.99[ASN][1000 genomes]
rs1377416	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1534576	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2203712	0.95[JPT][hapmap]
rs2242081	0.95[JPT][hapmap]
rs2278890	0.92[CEU][hapmap]
rs2293576	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2293579	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3740689	0.83[CHB][hapmap]
rs3740699	0.84[JPT][hapmap]
rs3824869	0.88[CEU][hapmap]
rs4434960	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61897431	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6485758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6485763	0.95[JPT][hapmap]
rs7104036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933019	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7947450	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7950696	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs874896	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs896817	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv975328	chr11:47446815-47471052	Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7103648		cis	Lymphoblastoid	GTEx
rs7103648	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs7103648	C1QTNF4	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47448600-47488400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:47453400-47469200	Weak transcription	Psoas Muscle	Psoas
3	chr11:47453400-47480000	Weak transcription	Thymus	Thymus
4	chr11:47456600-47463600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:47456600-47468600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr11:47457400-47480200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr11:47457400-47480800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:47457400-47488400	Weak transcription	Gastric	stomach
9	chr11:47457800-47469000	Weak transcription	Spleen	Spleen
10	chr11:47459400-47462000	Weak transcription	HSMM	muscle
11	chr11:47459800-47462200	Weak transcription	Fetal Muscle Leg	muscle
12	chr11:47459800-47463000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:47459800-47464000	Weak transcription	Brain Anterior Caudate	brain
14	chr11:47459800-47464400	Weak transcription	Left Ventricle	heart
15	chr11:47459800-47466400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:47459800-47469400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:47459800-47470800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:47459800-47480600	Weak transcription	Fetal Intestine Small	intestine
19	chr11:47459800-47480800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:47460000-47462400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr11:47460000-47464200	Weak transcription	Adipose Nuclei	Adipose
22	chr11:47460000-47470800	Weak transcription	Lung	lung
23	chr11:47460000-47475600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr11:47460400-47464800	Strong transcription	HSMMtube	muscle
25	chr11:47460600-47462200	Enhancers	HepG2	liver
26	chr11:47460600-47462600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr11:47460600-47462600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:47460600-47462600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:47460600-47465600	Weak transcription	Liver	Liver
30	chr11:47460600-47469200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr11:47461600-47464800	Strong transcription	Fetal Muscle Trunk	muscle

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