Variant report

Variant	rs17854829
Chromosome Location	chr12:57619359-57619360
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:57619249-57619360	GM19239	blood:	n/a	n/a
2	E2F6	chr12:57618393-57619760	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr12:57619240-57619490	HUVEC	blood vessel:	n/a	n/a
4	E2F6	chr12:57619277-57619536	K562	blood:	n/a	n/a
5	NFIC	chr12:57619100-57619782	ECC-1	luminal epithelium:	n/a	n/a
6	NFIC	chr12:57619077-57619871	ECC-1	luminal epithelium:	n/a	n/a
7	E2F6	chr12:57618406-57619893	H1-hESC	embryonic stem cell:	n/a	n/a
8	MTA3	chr12:57619168-57619559	GM12878	blood:	n/a	n/a
9	ZEB1	chr12:57619222-57619608	GM12878	blood:	n/a	chr12:57619365-57619374
10	MXI1	chr12:57619343-57619411	GM12878	blood:	n/a	n/a
11	MAX	chr12:57619158-57619554	K562	blood:	n/a	n/a
12	POLR2A	chr12:57619191-57619559	GM12878	blood:	n/a	n/a
13	PAX5	chr12:57619209-57619483	GM12878	blood:	n/a	n/a
14	MAX	chr12:57618452-57619615	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr12:57618679-57619550	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr12:57619220-57619370	GM12872	blood:	n/a	n/a
17	PAX5	chr12:57619208-57619448	GM12892	blood:	n/a	n/a
18	MAX	chr12:57619229-57619389	HepG2	liver:	n/a	n/a
19	BHLHE40	chr12:57619328-57619465	GM12878	blood:	n/a	n/a
20	MAX	chr12:57618390-57619602	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57583820..57586424-chr12:57618362..57620239,2	K562	blood:
2	chr12:57618582..57621121-chr12:57939441..57941129,2	K562	blood:
3	chr12:57481223..57483699-chr12:57618640..57620168,2	K562	blood:
4	chr12:57481223..57482967-chr12:57618329..57620140,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000202067	TF binding region
SHMT2	TF binding region
ENSG00000175203	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000166886	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11172219	1.00[EUR][1000 genomes]
rs11557166	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28365863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34248177	1.00[EUR][1000 genomes]
rs34950222	1.00[EUR][1000 genomes]
rs35021926	1.00[EUR][1000 genomes]
rs56273568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61978619	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62620661	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7304504	1.00[EUR][1000 genomes]
rs74093103	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74093104	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74093113	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74093115	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74093117	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1809338	chr12:57580227-57628338	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv899116	chr12:57597169-57623363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57611400-57623000	Weak transcription	Right Atrium	heart
2	chr12:57613200-57621800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:57613400-57620400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr12:57613400-57621600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
5	chr12:57613800-57620000	Bivalent Enhancer	Primary B cells from cord blood	blood
6	chr12:57615000-57622800	Weak transcription	A549	lung
7	chr12:57617200-57621400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr12:57617600-57620200	Weak transcription	K562	blood
9	chr12:57618000-57619600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:57618200-57619800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:57618200-57619800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
12	chr12:57618200-57620600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
13	chr12:57618200-57621200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr12:57618200-57621800	Bivalent Enhancer	Fetal Thymus	thymus
15	chr12:57618400-57619600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr12:57618400-57619800	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:57618400-57620000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:57618400-57620600	Enhancers	Pancreas	Pancrea
19	chr12:57618400-57620600	Enhancers	Spleen	Spleen
20	chr12:57618400-57620800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
21	chr12:57618400-57620800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
22	chr12:57618400-57621000	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr12:57618400-57621600	Bivalent Enhancer	Fetal Stomach	stomach
24	chr12:57618600-57619400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
25	chr12:57618600-57619600	Bivalent Enhancer	Fetal Heart	heart
26	chr12:57618600-57620000	Bivalent Enhancer	Fetal Intestine Small	intestine
27	chr12:57618600-57620400	Enhancers	Liver	Liver
28	chr12:57618600-57621200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
29	chr12:57618800-57619400	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:57618800-57619400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
31	chr12:57618800-57619600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
32	chr12:57618800-57619600	Enhancers	Right Ventricle	heart
33	chr12:57618800-57619600	Bivalent Enhancer	HUVEC	blood vessel
34	chr12:57618800-57619800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
35	chr12:57618800-57620000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:57618800-57621200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:57618800-57621200	Bivalent Enhancer	Fetal Brain Male	brain
38	chr12:57618800-57621400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
39	chr12:57618800-57621400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
40	chr12:57618800-57621600	Bivalent Enhancer	Fetal Intestine Large	intestine
41	chr12:57619000-57619400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
42	chr12:57619000-57619800	Bivalent Enhancer	Adipose Nuclei	Adipose
43	chr12:57619000-57619800	Bivalent Enhancer	Esophagus	oesophagus
44	chr12:57619000-57619800	Bivalent Enhancer	Placenta	Placenta
45	chr12:57619000-57619800	Enhancers	Gastric	stomach
46	chr12:57619000-57619800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
47	chr12:57619000-57619800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
48	chr12:57619000-57620000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
49	chr12:57619000-57620200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:57619000-57620400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood

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