Variant report

Variant	rs11609554
Chromosome Location	chr12:26112845-26112846
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	CTCF	chr12:26112720-26112870	AG09309	skin:	n/a	n/a
2	CTCF	chr12:26112721-26112860	Kidney_OC	kidney:	n/a	n/a
3	SIN3AK20	chr12:26111968-26112917	MCF-7	breast:	n/a	n/a
4	CTCF	chr12:26112718-26112851	LNCaP	prostate:	n/a	n/a
5	FOS	chr12:26112576-26112980	MCF10A-Er-Src	breast:	n/a	n/a
6	CTCF	chr12:26112720-26112870	RPTEC	kidney:	n/a	n/a
7	SMC3	chr12:26110022-26114054	SK-N-SH	brain:	n/a	chr12:26111781-26111791
8	CTCF	chr12:26112720-26112870	AG09319	gingival:	n/a	n/a
9	CTCF	chr12:26112700-26112850	HCPEpiC	choroid plexus:	n/a	n/a
10	CTCF	chr12:26112700-26112850	SK-N-SH_RA	brain:	n/a	n/a
11	CTCF	chr12:26112709-26112898	HUVEC	blood vessel:	n/a	n/a
12	RAD21	chr12:26110041-26114263	SK-N-SH	brain:	n/a	chr12:26111781-26111791
13	CHD2	chr12:26110731-26113022	Hela-S3	cervix:	n/a	chr12:26111241-26111251
14	POLR2A	chr12:26112573-26113500	PANC-1	pancreas:	n/a	n/a
15	CEBPB	chr12:26112527-26113059	A549	lung:	n/a	n/a
16	CTCF	chr12:26112720-26112870	HBMEC	blood vessel:	n/a	n/a
17	CTCF	chr12:26112740-26112890	HPF	lung:	n/a	n/a
18	CTCF	chr12:26112780-26112930	SAEC	small airway:	n/a	n/a
19	USF2	chr12:26112586-26112906	Hela-S3	cervix:	n/a	n/a
20	TAF1	chr12:26112482-26112874	SK-N-SH	brain:	n/a	n/a
21	CTCF	chr12:26112740-26112890	AoAF	blood vessel:	n/a	n/a
22	CTCF	chr12:26112760-26112910	BJ	skin:	n/a	n/a
23	CTCF	chr12:26112740-26112890	HCPEpiC	choroid plexus:	n/a	n/a
24	POLR2A	chr12:26111010-26112908	Hela-S3	cervix:	n/a	n/a
25	TBP	chr12:26112175-26113073	Hela-S3	cervix:	n/a	n/a
26	FOS	chr12:26112600-26112928	MCF10A-Er-Src	breast:	n/a	n/a
27	CTCF	chr12:26112737-26112898	LNCaP	prostate:	n/a	n/a
28	CTCF	chr12:26112720-26112870	HCM	heart:	n/a	n/a
29	POLR2A	chr12:26112533-26113064	U87	brain:	n/a	n/a
30	CTCF	chr12:26112720-26112870	HPF	lung:	n/a	n/a
31	CTCF	chr12:26112700-26112850	HUVEC	blood vessel:	n/a	n/a
32	SIN3AK20	chr12:26111019-26113072	PANC-1	pancreas:	n/a	n/a
33	TCF7L2	chr12:26112605-26113353	PANC-1	pancreas:	n/a	chr12:26113179-26113193 chr12:26113182-26113191
34	SMARCC1	chr12:26112076-26113448	Hela-S3	cervix:	n/a	n/a
35	MAX	chr12:26110853-26113036	Hela-S3	cervix:	n/a	chr12:26112239-26112249 chr12:26112912-26112920
36	CTCF	chr12:26112720-26112870	NHDF-neo	bronchial:	n/a	n/a
37	CEBPB	chr12:26112669-26112946	HepG2	liver:	n/a	n/a
38	POLR2A	chr12:26110826-26113301	HUVEC	blood vessel:	n/a	n/a
39	TAF1	chr12:26112463-26112902	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr12:26112493-26112983	ProgFib	skin:	n/a	n/a
41	POLR2A	chr12:26110543-26112977	HUVEC	blood vessel:	n/a	n/a
42	CTCF	chr12:26112760-26112910	HFF-Myc	foreskin:	n/a	n/a
43	POLR2A	chr12:26112760-26112960	H1-hESC	embryonic stem cell:	n/a	n/a
44	SIN3AK20	chr12:26112660-26113018	PFSK-1	brain:	n/a	n/a
45	CTCF	chr12:26111844-26113535	SK-N-SH	brain:	n/a	n/a
46	CTCF	chr12:26112700-26112850	HAc	cerebellar:	n/a	n/a
47	RFX5	chr12:26112147-26112883	Hela-S3	cervix:	n/a	n/a
48	MXI1	chr12:26110512-26114891	SK-N-SH	brain:	n/a	n/a
49	MAZ	chr12:26110601-26113503	IMR90	lung:	n/a	chr12:26112239-26112249 chr12:26110615-26110625 chr12:26112912-26112920
50	CTCF	chr12:26112715-26112850	Fibrobl	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25986954..25988487-chr12:26111623..26114201,2	MCF-7	breast:

Variant related genes	Relation type
RASSF8-AS1	TF binding region
ENSG00000256440	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11610085	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11610628	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6487520	0.91[AMR][1000 genomes];0.87[EUR][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	esv2758300	chr12:25992331-26161116	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	esv2759886	chr12:25992331-26161116	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	esv17456	chr12:26108846-26114910	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv3337985	chr12:26109585-26113883	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv3385039	chr12:26110185-26113083	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv3323230	chr12:26110310-26112858	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv3366350	chr12:26110485-26113208	Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3405562	chr12:26110910-26113458	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26110000-26113600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:26110200-26113400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:26110200-26115200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:26110400-26113200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:26110400-26113200	Active TSS	Fetal Muscle Trunk	muscle
6	chr12:26110400-26113400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr12:26110400-26113400	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr12:26110400-26113400	Active TSS	Fetal Kidney	kidney
9	chr12:26110400-26113600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:26110400-26114000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr12:26110400-26114400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:26110600-26113000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr12:26110600-26113000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:26110600-26113000	Active TSS	Brain Substantia Nigra	brain
15	chr12:26110600-26113200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:26110600-26113200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:26110600-26113200	Active TSS	Fetal Lung	lung
18	chr12:26110600-26113200	Active TSS	Left Ventricle	heart
19	chr12:26110600-26113200	Active TSS	HSMM	muscle
20	chr12:26110600-26113400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:26110600-26113400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr12:26110600-26113400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:26110600-26113400	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr12:26110600-26113400	Active TSS	Aorta	Aorta
25	chr12:26110600-26113400	Active TSS	Brain Angular Gyrus	brain
26	chr12:26110600-26113600	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr12:26110600-26113600	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr12:26110600-26113600	Active TSS	Rectal Smooth Muscle	rectum
29	chr12:26110600-26113600	Active TSS	NHDF-Ad	bronchial
30	chr12:26110600-26113800	Active TSS	Right Ventricle	heart
31	chr12:26110600-26114000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:26110600-26114000	Active TSS	Right Atrium	heart
33	chr12:26110800-26113200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:26110800-26113200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:26110800-26113200	Active TSS	Muscle Satellite Cultured Cells	--
36	chr12:26110800-26113200	Active TSS	Brain Hippocampus Middle	brain
37	chr12:26110800-26113200	Active TSS	Psoas Muscle	Psoas
38	chr12:26110800-26113200	Active TSS	HMEC	breast
39	chr12:26110800-26113400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:26110800-26113400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:26110800-26113400	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr12:26110800-26113400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:26110800-26113400	Active TSS	Brain Anterior Caudate	brain
44	chr12:26110800-26113400	Active TSS	Colon Smooth Muscle	Colon
45	chr12:26110800-26113600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:26110800-26113600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:26110800-26113800	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr12:26110800-26113800	Active TSS	Ovary	ovary
49	chr12:26110800-26114600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:26111000-26113000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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