Variant report

Variant	rs10896129
Chromosome Location	chr11:66338300-66338301
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	REST	chr11:66337667-66338502	H1-neurons	neurons:	n/a	n/a
2	REST	chr11:66337627-66338800	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr11:66337703-66338488	H1-neurons	neurons:	n/a	n/a
4	TAF1	chr11:66337910-66338421	H1-neurons	neurons:	n/a	n/a
5	TAF1	chr11:66337674-66338365	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD1	chr11:66337988-66338366	H1-hESC	embryonic stem cell:	n/a	n/a
7	TEAD4	chr11:66337552-66338340	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr11:66337714-66338422	H1-hESC	embryonic stem cell:	n/a	n/a
9	TBP	chr11:66337668-66338316	H1-hESC	embryonic stem cell:	n/a	n/a
10	TEAD4	chr11:66337580-66338349	H1-hESC	embryonic stem cell:	n/a	n/a
11	CEBPB	chr11:66337601-66338315	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr11:66337807-66338470	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr11:66337436-66338802	H1-hESC	embryonic stem cell:	n/a	n/a

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

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

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10501397	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896124	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896125	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227495	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227497	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11227498	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227499	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227500	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227501	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227502	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227503	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227509	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227510	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227511	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227512	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227514	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227515	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227522	0.88[EUR][1000 genomes]
rs11227523	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227525	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11227527	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11227534	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11550299	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11821155	0.90[EUR][1000 genomes]
rs11822028	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11822099	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11824771	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12099041	0.90[EUR][1000 genomes]
rs12221821	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12223479	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12272545	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17065	0.97[EUR][1000 genomes]
rs17147644	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17496250	0.97[EUR][1000 genomes]
rs17496586	0.95[EUR][1000 genomes]
rs17580784	0.84[EUR][1000 genomes]
rs2075792	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276406	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2277302	0.90[EUR][1000 genomes]
rs2279864	0.90[EUR][1000 genomes]
rs2279865	0.84[EUR][1000 genomes]
rs2298806	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2305532	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2305533	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2305534	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305535	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28414721	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3179961	0.89[EUR][1000 genomes]
rs35733139	0.87[EUR][1000 genomes]
rs3737525	0.98[EUR][1000 genomes]
rs3741360	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3816492	0.97[EUR][1000 genomes]
rs3819247	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3825065	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3892818	0.90[EUR][1000 genomes]
rs4542420	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4576	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4630309	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4930182	0.84[EUR][1000 genomes]
rs4930183	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4930377	0.89[EUR][1000 genomes]
rs4930378	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4930379	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4930380	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56144989	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57045447	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57207756	0.95[EUR][1000 genomes]
rs57288351	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57596493	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57634456	0.93[EUR][1000 genomes]
rs57691879	0.90[EUR][1000 genomes]
rs57724777	0.90[EUR][1000 genomes]
rs59829960	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59982644	0.98[EUR][1000 genomes]
rs60358007	0.87[EUR][1000 genomes]
rs60645853	0.98[EUR][1000 genomes]
rs61561111	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61582507	0.86[EUR][1000 genomes]
rs7104378	0.84[EUR][1000 genomes]
rs7116921	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7116940	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7123176	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7928882	0.87[EUR][1000 genomes]
rs7939759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943327	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7950407	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7950790	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10896129	CCS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 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	chr11:66337600-66338600	Enhancers	H9 Cell Line	embryonic stem cell
9	chr11:66337600-66338600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr11:66337600-66338600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr11:66337600-66338600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr11:66337600-66338800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:66337600-66338800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:66337600-66338800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:66337600-66338800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr11:66337800-66338400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr11:66337800-66338600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:66337800-66338600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:66337800-66338800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr11:66337800-66338800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:66337800-66338800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:66338000-66338600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr11:66338000-66338600	Enhancers	Fetal Kidney	kidney
24	chr11:66338200-66338400	Enhancers	HUES6 Cell Line	embryonic stem cell

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