Variant report

Variant	rs560556
Chromosome Location	chr11:66338118-66338119
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr11:66337667-66338502	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr11:66337670-66338270	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr11:66337627-66338800	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr11:66337703-66338488	H1-neurons	neurons:	n/a	n/a
5	TAF1	chr11:66337910-66338421	H1-neurons	neurons:	n/a	n/a
6	CEBPB	chr11:66337842-66338144	HepG2	liver:	n/a	n/a
7	TAF1	chr11:66337674-66338365	H1-hESC	embryonic stem cell:	n/a	n/a
8	CHD1	chr11:66337988-66338366	H1-hESC	embryonic stem cell:	n/a	n/a
9	TEAD4	chr11:66337552-66338340	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr11:66337714-66338422	H1-hESC	embryonic stem cell:	n/a	n/a
11	TBP	chr11:66337668-66338316	H1-hESC	embryonic stem cell:	n/a	n/a
12	TEAD4	chr11:66337580-66338349	H1-hESC	embryonic stem cell:	n/a	n/a
13	CEBPB	chr11:66337601-66338315	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr11:66337807-66338470	H1-neurons	neurons:	n/a	n/a
15	POLR2A	chr11:66337436-66338802	H1-hESC	embryonic stem cell:	n/a	n/a
16	GTF2F1	chr11:66338081-66338238	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66311475..66316022-chr11:66335981..66338223,4	MCF-7	breast:
2	chr11:66338015..66339949-chr11:66360318..66361914,2	MCF-7	breast:

No data

Variant related genes	Relation type
CTSF	TF binding region
ENSG00000173992	Chromatin interaction
ENSG00000182791	Chromatin interaction
ENSG00000174165	Chromatin interaction
ENSG00000248746	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10736656	0.84[ASN][1000 genomes]
rs10791882	0.93[ASN][1000 genomes]
rs1127894	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12577111	0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.80[YRI][hapmap]
rs12805133	0.92[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs1671062	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.84[ASN][1000 genomes]
rs1671063	0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs1671064	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1671065	0.84[ASN][1000 genomes]
rs1700189	0.82[ASN][1000 genomes]
rs1791684	0.91[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs1791686	0.86[ASN][1000 genomes]
rs1815739	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2000939	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276138	0.83[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs2279863	0.90[JPT][hapmap]
rs3018318	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3741363	0.81[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs474602	1.00[YRI][hapmap]
rs486584	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.80[YRI][hapmap];0.92[ASN][1000 genomes]
rs4930387	0.83[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs498045	0.88[GIH][hapmap]
rs503250	0.83[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs508443	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs509556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs531490	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs535211	0.83[ASW][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs540874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs545009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs556759	0.83[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs572846	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs577023	0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap]
rs580910	0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.80[YRI][hapmap]
rs615205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618838	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs630021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs662094	0.83[AFR][1000 genomes]
rs677488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs678397	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs692892	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7925108	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs8432	0.82[CHB][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.80[YRI][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv897787	chr11:66300348-66347850	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv897788	chr11:66319262-66347850	Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs560556	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs560556	YIF1A	cis	parietal	SCAN
rs560556	CCS	cis	multi-tissue	Pritchard
rs560556	YIF1A	cis	cerebellum	SCAN
rs560556	ACTN3	cis	Muscle Skeletal	GTEx
rs560556	CTSF	cis	cerebellum	SCAN
rs560556	CDC42EP2	cis	cerebellum	SCAN
rs560556	CCDC85B	cis	parietal	SCAN
rs560556	CTSF	cis	parietal	SCAN
rs560556	UNC93B1	cis	cerebellum	SCAN
rs560556	PRDX5	cis	cerebellum	SCAN
rs560556	CCS	cis	lymphoblastoid	seeQTL
rs560556	GANAB	cis	parietal	SCAN
rs560556	KDM2A	cis	cerebellum	SCAN
rs560556	ACTN3	cis	lymphoblastoid	seeQTL
rs560556	SYT12	cis	parietal	SCAN
rs560556	CTD-3074O7.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66336200-66338400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:66336400-66346600	Weak transcription	Right Atrium	heart
3	chr11:66336800-66338800	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr11:66336800-66338800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr11:66336800-66338800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr11:66337000-66346600	Weak transcription	K562	blood
7	chr11:66337400-66338400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:66337600-66338200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:66337600-66338600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr11:66337600-66338600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr11:66337600-66338600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr11:66337600-66338600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:66337600-66338800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:66337600-66338800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:66337600-66338800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:66337600-66338800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr11:66337800-66338200	Enhancers	HSMMtube	muscle
18	chr11:66337800-66338400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr11:66337800-66338600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:66337800-66338600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:66337800-66338800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr11:66337800-66338800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:66337800-66338800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr11:66338000-66338200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr11:66338000-66338600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr11:66338000-66338600	Enhancers	Fetal Kidney	kidney

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