Variant report

Variant	rs11229101
Chromosome Location	chr11:57479101-57479102
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	GTF3C2	chr11:57478738-57479207	Hela-S3	cervix:	n/a	n/a
2	MAX	chr11:57479099-57480555	ECC-1	luminal epithelium:	n/a	n/a
3	MXI1	chr11:57478662-57480846	IMR90	lung:	n/a	n/a
4	CREB1	chr11:57479023-57480405	A549	lung:	n/a	n/a
5	POLR2A	chr11:57478868-57480666	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr11:57479076-57480400	Hela-S3	cervix:	n/a	n/a
7	HCFC1	chr11:57478908-57481423	Hela-S3	cervix:	n/a	n/a
8	SIN3A	chr11:57479031-57480660	H1-hESC	embryonic stem cell:	n/a	n/a
9	REST	chr11:57478992-57480794	H1-neurons	neurons:	n/a	chr11:57479293-57479300
10	CEBPB	chr11:57478956-57479586	H1-hESC	embryonic stem cell:	n/a	chr11:57479401-57479409
11	MAX	chr11:57479083-57480519	SK-N-SH	brain:	n/a	n/a
12	YY1	chr11:57479101-57480480	SK-N-SH_RA	brain:	n/a	chr11:57479725-57479734 chr11:57480086-57480098
13	MAX	chr11:57479044-57480545	HepG2	liver:	n/a	n/a
14	POLR2A	chr11:57478986-57480338	Hela-S3	cervix:	n/a	n/a
15	SIN3AK20	chr11:57478946-57480537	MCF-7	breast:	n/a	n/a
16	MAX	chr11:57478989-57480678	K562	blood:	n/a	n/a
17	SIN3AK20	chr11:57479022-57479874	PANC-1	pancreas:	n/a	n/a
18	SIN3AK20	chr11:57479075-57479941	MCF-7	breast:	n/a	n/a
19	SIN3AK20	chr11:57479039-57479454	H1-hESC	embryonic stem cell:	n/a	n/a
20	CREB1	chr11:57479038-57480527	HepG2	liver:	n/a	n/a
21	SIN3AK20	chr11:57479058-57479380	A549	lung:	n/a	n/a
22	TCF12	chr11:57479036-57480505	A549	lung:	n/a	n/a
23	NR2F2	chr11:57478955-57480605	K562	blood:	n/a	n/a
24	SP1	chr11:57479072-57480313	H1-hESC	embryonic stem cell:	n/a	chr11:57479372-57479382 chr11:57479656-57479667 chr11:57479726-57479737 chr11:57479726-57479738 chr11:57480035-57480047 chr11:57479372-57479382 chr11:57480035-57480047 chr11:57480036-57480045 chr11:57480032-57480046 chr11:57480037-57480046 chr11:57479390-57479411
25	NFYB	chr11:57478783-57480272	Hela-S3	cervix:	n/a	chr11:57479397-57479412 chr11:57479399-57479412 chr11:57479696-57479710 chr11:57479911-57479926 chr11:57479398-57479412 chr11:57479914-57479927 chr11:57479397-57479412
26	SIN3AK20	chr11:57479036-57479720	K562	blood:	n/a	n/a
27	POLR2A	chr11:57479092-57480749	GM12892	blood:	n/a	n/a
28	CEBPB	chr11:57478959-57479132	K562	blood:	n/a	n/a
29	SRF	chr11:57479089-57480615	HCT-116	colon:	n/a	chr11:57480031-57480041
30	POLR2A	chr11:57479039-57480892	HL-60	blood:	n/a	n/a
31	POLR2A	chr11:57478964-57480588	GM12878	blood:	n/a	n/a
32	POLR2A	chr11:57479101-57479824	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr11:57478849-57480792	K562	blood:	n/a	n/a
34	SIN3AK20	chr11:57479030-57479889	H1-hESC	embryonic stem cell:	n/a	n/a
35	GABPA	chr11:57479034-57480639	SK-N-SH	brain:	n/a	chr11:57479213-57479222
36	SP1	chr11:57478972-57480661	HCT-116	colon:	n/a	chr11:57479372-57479382 chr11:57479656-57479667 chr11:57479726-57479737 chr11:57479726-57479738 chr11:57480035-57480047 chr11:57479372-57479382 chr11:57480035-57480047 chr11:57480036-57480045 chr11:57480032-57480046 chr11:57480037-57480046 chr11:57479390-57479411
37	POLR2A	chr11:57478962-57480602	K562	blood:	n/a	n/a
38	POLR2A	chr11:57479089-57480454	GM12892	blood:	n/a	n/a
39	CBX3	chr11:57479004-57480334	K562	blood:	n/a	n/a
40	TEAD4	chr11:57479019-57480522	K562	blood:	n/a	n/a
41	ZNF263	chr11:57479069-57479588	HEK293-T-REx	kidney:	n/a	n/a
42	POLR2A	chr11:57479025-57480590	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr11:57479048-57480497	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr11:57479060-57479829	U87	brain:	n/a	n/a
45	POLR2A	chr11:57478808-57480429	K562	blood:	n/a	n/a
46	RCOR1	chr11:57479064-57480281	K562	blood:	n/a	n/a
47	SIN3A	chr11:57479085-57480373	GM12878	blood:	n/a	n/a
48	POLR2A	chr11:57479033-57479838	A549	lung:	n/a	n/a
49	POLR2A	chr11:57479065-57480547	MCF-7	breast:	n/a	n/a
50	POLR2A	chr11:57479033-57480514	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:57416825..57418474-chr11:57477020..57479617,2	K562	blood:
2	chr11:57477767..57479895-chr11:57568305..57570936,2	K562	blood:
3	chr11:57435266..57437517-chr11:57478547..57480108,2	MCF-7	breast:
4	chr11:57478792..57480294-chr11:57529805..57532617,2	K562	blood:
5	chr11:57296138..57298827-chr11:57479075..57481840,2	K562	blood:
6	chr11:57478353..57481972-chr11:57506953..57510365,5	MCF-7	breast:
7	chr11:57478395..57480567-chr11:57567397..57569805,2	K562	blood:
8	chr11:57433212..57437810-chr11:57477098..57481918,8	MCF-7	breast:
9	chr11:57478095..57482223-chr11:57507421..57512003,5	K562	blood:
10	chr11:57447901..57451282-chr11:57477513..57480655,3	K562	blood:
11	chr11:57478057..57480948-chr11:57506438..57510938,4	MCF-7	breast:
12	chr11:57471016..57472571-chr11:57477897..57479622,2	MCF-7	breast:
13	chr11:57478095..57481312-chr11:57507421..57511942,8	K562	blood:
14	chr11:57433936..57437289-chr11:57477964..57482818,9	K562	blood:
15	chr11:57433884..57439071-chr11:57477629..57483930,15	K562	blood:

Variant related genes	Relation type
TMX2-CTNND1	TF binding region
TMX2	TF binding region
ENSG00000198561	Chromatin interaction
ENSG00000134809	Chromatin interaction
ENSG00000156599	Chromatin interaction
ENSG00000211450	Chromatin interaction
ENSG00000166793	Chromatin interaction
ENSG00000254732	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10128604	0.83[AFR][1000 genomes]
rs11229100	0.91[AFR][1000 genomes]
rs12292393	0.90[AFR][1000 genomes]
rs17152027	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	nsv975360	chr11:57466716-57480320	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57478200-57479200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr11:57478200-57479400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr11:57478400-57479200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:57478400-57479200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:57478400-57479200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:57478400-57479200	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr11:57478400-57479400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:57478400-57479400	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr11:57478400-57479400	Flanking Active TSS	Dnd41	blood
10	chr11:57478400-57480800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:57478400-57481200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:57478400-57481800	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr11:57478600-57479200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr11:57478600-57479200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr11:57478600-57479200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr11:57478600-57479200	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr11:57478600-57479200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr11:57478600-57479200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:57478600-57479200	Flanking Active TSS	Brain Substantia Nigra	brain
20	chr11:57478600-57479200	Flanking Active TSS	Colonic Mucosa	Colon
21	chr11:57478600-57479200	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr11:57478600-57479200	Flanking Active TSS	HUVEC	blood vessel
23	chr11:57478600-57479400	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr11:57478600-57479400	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr11:57478600-57479400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
26	chr11:57478600-57479400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr11:57478600-57479400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr11:57478600-57480800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:57478600-57480800	Active TSS	HSMMtube	muscle
30	chr11:57478600-57480800	Active TSS	NHLF	lung
31	chr11:57478600-57481000	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr11:57478600-57481000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr11:57478600-57481000	Active TSS	HSMM	muscle
34	chr11:57478600-57481200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:57478600-57481200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr11:57478600-57481400	Active TSS	H9 Cell Line	embryonic stem cell
37	chr11:57478600-57481600	Active TSS	K562	blood
38	chr11:57478600-57481800	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr11:57478800-57479200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:57478800-57479200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:57478800-57479200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr11:57478800-57479200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr11:57478800-57479200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr11:57478800-57479200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr11:57478800-57479200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr11:57478800-57479200	Flanking Active TSS	Esophagus	oesophagus
47	chr11:57478800-57479200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr11:57478800-57479200	Flanking Active TSS	Fetal Heart	heart
49	chr11:57478800-57479200	Flanking Active TSS	Fetal Lung	lung
50	chr11:57478800-57479200	Flanking Active TSS	Fetal Muscle Trunk	muscle

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