Variant report

Variant	rs2742506
Chromosome Location	chr11:8956845-8956846
allele	A/G
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	RFX5	chr11:8956299-8957103	Hela-S3	cervix:	n/a	n/a
2	GATA3	chr11:8956123-8956906	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr11:8956700-8956850	HEEpiC	esophagus:	n/a	chr11:8956746-8956762
4	USF2	chr11:8956405-8956893	Hela-S3	cervix:	n/a	n/a
5	EP300	chr11:8956322-8956849	Hela-S3	cervix:	n/a	chr11:8956764-8956773
6	KAP1	chr11:8956290-8957049	U2OS	brain:	n/a	n/a
7	TCF12	chr11:8956258-8956880	SK-N-SH	brain:	n/a	n/a
8	TBL1XR1	chr11:8956805-8956846	K562	blood:	n/a	n/a
9	CTCF	chr11:8956780-8956930	HEK293	kidney:	n/a	n/a
10	RAD21	chr11:8956354-8956987	Hela-S3	cervix:	n/a	n/a
11	TCF7L2	chr11:8956380-8956903	HCT-116	colon:	n/a	n/a
12	RCOR1	chr11:8956281-8956905	Hela-S3	cervix:	n/a	n/a
13	JUND	chr11:8956237-8956875	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr11:8956047-8956880	SK-N-SH	brain:	n/a	n/a
15	CEBPB	chr11:8956342-8956936	Hela-S3	cervix:	n/a	n/a
16	ZNF263	chr11:8956286-8956912	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8955859..8958646-chr11:8984465..8986441,3	MCF-7	breast:
2	chr11:8955484..8958608-chr11:8984431..8986354,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKIP1-6	chr11:8956716-8957048	NONHSAT017892

Variant related genes	Relation type
C11orf16	TF binding region
ENSG00000175348	Chromatin interaction
ENSG00000254860	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10400349	0.84[ASN][1000 genomes]
rs11042113	0.93[ASN][1000 genomes]
rs12574321	1.00[AMR][1000 genomes]
rs1432117	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1432118	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2116513	0.88[ASN][1000 genomes]
rs2163627	0.88[ASN][1000 genomes]
rs2436176	0.83[ASN][1000 genomes]
rs2568022	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2568040	0.88[ASN][1000 genomes]
rs2568067	0.88[ASN][1000 genomes]
rs2568073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2568076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2568084	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2653572	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2653599	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2653617	0.88[ASN][1000 genomes]
rs2742481	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2742490	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2742492	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2742509	1.00[ASN][1000 genomes]
rs2742522	0.93[ASN][1000 genomes]
rs4910179	0.98[ASN][1000 genomes]
rs56947653	0.95[ASN][1000 genomes]

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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv8787	chr11:8954949-8959098	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8942400-8959000	Weak transcription	Fetal Kidney	kidney
2	chr11:8943800-8969200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr11:8944600-8985000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:8945800-8974000	Weak transcription	Colon Smooth Muscle	Colon
5	chr11:8947000-8968800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:8947000-8977000	Weak transcription	Aorta	Aorta
7	chr11:8947400-8969000	Weak transcription	Thymus	Thymus
8	chr11:8947600-8969000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr11:8948200-8969000	Weak transcription	Fetal Brain Female	brain
10	chr11:8948600-8969200	Weak transcription	Gastric	stomach
11	chr11:8948600-8969200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr11:8951200-8974400	Weak transcription	HepG2	liver
13	chr11:8952600-8957200	Weak transcription	Spleen	Spleen
14	chr11:8952600-8975800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:8952800-8968600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:8954400-8984400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:8955200-8976200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:8955600-8958200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr11:8955800-8968000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:8956200-8957000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr11:8956200-8957000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:8956200-8957000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr11:8956200-8957000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr11:8956200-8957000	Flanking Active TSS	Hela-S3	cervix
25	chr11:8956200-8957000	Enhancers	HSMM	muscle
26	chr11:8956200-8957200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr11:8956200-8957200	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr11:8956200-8957200	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr11:8956200-8957200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:8956200-8957400	Enhancers	K562	blood
31	chr11:8956200-8957400	Enhancers	NHDF-Ad	bronchial
32	chr11:8956400-8957000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:8956400-8957000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr11:8956400-8957000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:8956400-8957000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr11:8956400-8957000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:8956400-8957000	Enhancers	Fetal Heart	heart
38	chr11:8956400-8957000	Enhancers	Fetal Intestine Large	intestine
39	chr11:8956400-8957000	Enhancers	HSMMtube	muscle
40	chr11:8956400-8957000	Flanking Active TSS	NHLF	lung
41	chr11:8956400-8957200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr11:8956400-8957200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:8956400-8957400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:8956400-8957400	Enhancers	Placenta	Placenta
45	chr11:8956600-8957000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr11:8956600-8957000	Enhancers	Fetal Stomach	stomach
47	chr11:8956600-8957000	Flanking Active TSS	NH-A	brain
48	chr11:8956600-8957200	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr11:8956800-8957200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:8956800-8957200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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