Variant report

Variant	rs12694100
Chromosome Location	chr2:209121189-209121190
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	chr2:209121107-209121515	HepG2	liver:	n/a	chr2:209121335-209121351 chr2:209121339-209121349 chr2:209121336-209121357 chr2:209121334-209121352
2	RAD21	chr2:209121132-209121517	HepG2	liver:	n/a	chr2:209121340-209121350 chr2:209121339-209121348 chr2:209121338-209121351 chr2:209121340-209121352 chr2:209121335-209121354
3	EBF1	chr2:209121189-209121493	GM12878	blood:	n/a	n/a
4	RAD21	chr2:209121184-209121477	GM12878	blood:	n/a	chr2:209121340-209121350 chr2:209121339-209121348 chr2:209121338-209121351 chr2:209121340-209121352 chr2:209121335-209121354
5	CTCF	chr2:209121180-209121330	A549	lung:	n/a	n/a
6	CTCF	chr2:209121152-209121506	K562	blood:	n/a	chr2:209121335-209121351 chr2:209121339-209121349 chr2:209121336-209121357 chr2:209121334-209121352
7	TEAD4	chr2:209121052-209121535	HepG2	liver:	n/a	n/a
8	CTCF	chr2:209121080-209121630	HCT-116	colon:	n/a	chr2:209121335-209121351 chr2:209121339-209121349 chr2:209121336-209121357 chr2:209121334-209121352
9	CTCF	chr2:209121147-209121522	GM12878	blood:	n/a	chr2:209121335-209121351 chr2:209121339-209121349 chr2:209121336-209121357 chr2:209121334-209121352
10	RAD21	chr2:209121163-209121496	HepG2	liver:	n/a	chr2:209121340-209121350 chr2:209121339-209121348 chr2:209121338-209121351 chr2:209121340-209121352 chr2:209121335-209121354
11	CTCF	chr2:209121152-209121510	MCF-7	breast:	n/a	chr2:209121335-209121351 chr2:209121339-209121349 chr2:209121336-209121357 chr2:209121334-209121352
12	POLR2A	chr2:209121074-209121250	HepG2	liver:	n/a	n/a
13	MYBL2	chr2:209118259-209121792	HepG2	liver:	n/a	n/a
14	CTCF	chr2:209121174-209121412	H1-hESC	embryonic stem cell:	n/a	chr2:209121335-209121351 chr2:209121339-209121349 chr2:209121336-209121357 chr2:209121334-209121352
15	RAD21	chr2:209121072-209121535	HCT-116	colon:	n/a	chr2:209121340-209121350 chr2:209121339-209121348 chr2:209121338-209121351 chr2:209121340-209121352 chr2:209121335-209121354
16	RAD21	chr2:209121156-209121524	ECC-1	luminal epithelium:	n/a	chr2:209121340-209121350 chr2:209121339-209121348 chr2:209121338-209121351 chr2:209121340-209121352 chr2:209121335-209121354
17	CTCF	chr2:209121120-209121270	BJ	skin:	n/a	n/a
18	RAD21	chr2:209121144-209121433	SK-N-SH_RA	brain:	n/a	chr2:209121340-209121350 chr2:209121339-209121348 chr2:209121338-209121351 chr2:209121340-209121352 chr2:209121335-209121354
19	CTCF	chr2:209121096-209121648	A549	lung:	n/a	chr2:209121335-209121351 chr2:209121339-209121349 chr2:209121336-209121357 chr2:209121334-209121352

No.	Distal block	Cell Line	Cell type
1	chr2:209117138..209121626-chr2:209129108..209132782,7	MCF-7	breast:
2	chr2:209119923..209123053-chr2:209129009..209130826,3	MCF-7	breast:
3	chr2:209116323..209122695-chr2:209127326..209132568,14	K562	blood:
4	chr2:209116323..209123332-chr2:209127326..209134005,17	K562	blood:
5	chr2:209118313..209121811-chr2:209130870..209135068,6	MCF-7	breast:

Variant related genes	Relation type
IDH1	TF binding region
ENSG00000115020	Chromatin interaction
ENSG00000228380	Chromatin interaction
ENSG00000138413	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11895188	0.91[EUR][1000 genomes]
rs12694101	0.96[EUR][1000 genomes]
rs13392540	0.82[AMR][1000 genomes]
rs59522113	0.92[EUR][1000 genomes]
rs67171462	0.91[EUR][1000 genomes]
rs6725418	0.93[EUR][1000 genomes]
rs67581965	0.93[EUR][1000 genomes]
rs73070962	0.93[EUR][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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS 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	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209120400-209121200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:209120400-209122000	Weak transcription	Aorta	Aorta
3	chr2:209120400-209122400	Active TSS	HepG2	liver
4	chr2:209120400-209123200	Enhancers	Fetal Heart	heart
5	chr2:209120600-209121200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:209120600-209121200	Enhancers	Primary B cells from peripheral blood	blood
7	chr2:209120600-209121200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr2:209120600-209121200	Enhancers	Brain Substantia Nigra	brain
9	chr2:209120600-209121200	Enhancers	Left Ventricle	heart
10	chr2:209120600-209121600	Weak transcription	Right Ventricle	heart
11	chr2:209120600-209121800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:209120600-209121800	Weak transcription	Pancreas	Pancrea
13	chr2:209120600-209122000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:209120600-209122000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:209120600-209122000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:209120600-209122000	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:209120600-209122000	Weak transcription	Fetal Lung	lung
18	chr2:209120600-209122000	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:209120600-209122000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:209120600-209122400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr2:209120600-209122600	Enhancers	Brain Angular Gyrus	brain
22	chr2:209120600-209122800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:209120600-209122800	Enhancers	Liver	Liver
24	chr2:209120600-209122800	Enhancers	Fetal Intestine Small	intestine
25	chr2:209120600-209123000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:209120800-209121200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:209120800-209121200	Enhancers	NHEK	skin
28	chr2:209120800-209121400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:209120800-209121400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:209120800-209121400	Weak transcription	Fetal Stomach	stomach
31	chr2:209120800-209121400	Enhancers	GM12878-XiMat	blood
32	chr2:209120800-209121600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:209120800-209121800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:209120800-209121800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:209120800-209121800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:209120800-209121800	Weak transcription	Fetal Kidney	kidney
37	chr2:209120800-209121800	Weak transcription	K562	blood
38	chr2:209120800-209122000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:209120800-209122000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:209120800-209122000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:209120800-209122000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:209120800-209122000	Weak transcription	Colonic Mucosa	Colon
43	chr2:209120800-209122200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr2:209120800-209122400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:209120800-209122600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr2:209120800-209123000	Enhancers	Fetal Intestine Large	intestine
47	chr2:209120800-209129800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr2:209121000-209121200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:209121000-209121400	Weak transcription	Rectal Mucosa Donor 31	rectum

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