Variant report

Variant	rs56206858
Chromosome Location	chr2:96933353-96933354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:96933260-96933410	GM12866	blood:	n/a	n/a
2	RAD21	chr2:96932764-96933357	HCT-116	colon:	n/a	n/a
3	POLR2A	chr2:96932861-96933800	GM12878	blood:	n/a	n/a
4	USF2	chr2:96933038-96933356	HepG2	liver:	n/a	n/a
5	NRF1	chr2:96933158-96933411	GM12878	blood:	n/a	n/a
6	RAD21	chr2:96932804-96933386	HCT-116	colon:	n/a	n/a
7	RAD21	chr2:96932713-96933599	SK-N-SH	brain:	n/a	n/a
8	MAFK	chr2:96933017-96933468	HepG2	liver:	n/a	n/a
9	CTCF	chr2:96933320-96933470	WI-38	lung:	n/a	n/a
10	POLR2A	chr2:96932796-96933497	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:96932944-96933492	HepG2	liver:	n/a	n/a
12	USF2	chr2:96933301-96933408	K562	blood:	n/a	n/a
13	CTCF	chr2:96931404-96933476	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr2:96932832-96933382	HCT-116	colon:	n/a	n/a
15	CTCF	chr2:96932804-96933399	A549	lung:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:96923812..96929557-chr2:96929618..96934014,11	K562	blood:
2	chr2:96929992..96934856-chr2:96999935..97004454,8	K562	blood:
3	chr2:96871739..96877156-chr2:96928674..96935050,17	K562	blood:
4	chr2:96781170..96783829-chr2:96932925..96934478,2	MCF-7	breast:
5	chr2:96930218..96933448-chr2:96968870..96972894,6	MCF-7	breast:
6	chr2:96930374..96934423-chr2:97000506..97002803,4	MCF-7	breast:
7	chr2:96868913..96876440-chr2:96928017..96934530,23	K562	blood:
8	chr2:96932066..96934505-chr2:97010263..97012552,2	MCF-7	breast:
9	chr2:96928652..96934635-chr2:96966746..96973769,11	K562	blood:
10	chr2:96930148..96938607-chr2:96966008..96973188,21	MCF-7	breast:
11	chr2:96871572..96876906-chr2:96928916..96935631,15	MCF-7	breast:
12	chr2:96870309..96876262-chr2:96928720..96933891,16	MCF-7	breast:
13	chr2:96929774..96935946-chr2:96940519..96946631,7	K562	blood:
14	chr2:96809057..96813419-chr2:96930542..96933437,6	MCF-7	breast:
15	chr2:96930650..96934516-chr2:96954888..96957639,4	MCF-7	breast:
16	chr2:96862732..96864612-chr2:96933173..96934680,2	K562	blood:

No data

Variant related genes	Relation type
TMEM127	TF binding region
ENSG00000228873	Chromatin interaction
ENSG00000144028	Chromatin interaction
ENSG00000222040	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000135956	Chromatin interaction
ENSG00000158050	Chromatin interaction
ENSG00000121152	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10167824	1.00[EUR][1000 genomes]
rs10168350	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10172762	1.00[EUR][1000 genomes]
rs10195177	1.00[EUR][1000 genomes]
rs10205464	1.00[EUR][1000 genomes]
rs13389648	1.00[EUR][1000 genomes]
rs13390615	1.00[EUR][1000 genomes]
rs13402791	1.00[EUR][1000 genomes]
rs13404944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13410507	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13410926	1.00[EUR][1000 genomes]
rs55845625	1.00[EUR][1000 genomes]
rs56225135	1.00[EUR][1000 genomes]
rs60864960	1.00[EUR][1000 genomes]
rs7565104	1.00[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	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription 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	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 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	chr2:96930400-96933400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr2:96930800-96933400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr2:96931600-96933600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
4	chr2:96932200-96933400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:96932200-96933800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:96932600-96933400	Enhancers	Fetal Brain Male	brain
7	chr2:96932600-96933600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr2:96932600-96933600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:96932600-96933600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr2:96932600-96933600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:96932600-96933600	Enhancers	Stomach Mucosa	stomach
12	chr2:96932600-96934000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr2:96932600-96934200	Weak transcription	Aorta	Aorta
14	chr2:96932600-96941600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:96932800-96933400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:96932800-96933400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr2:96932800-96933400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:96932800-96933400	Transcr. at gene 5' and 3'	Brain Anterior Caudate	brain
19	chr2:96932800-96933400	Flanking Active TSS	Colonic Mucosa	Colon
20	chr2:96932800-96933400	Flanking Active TSS	Fetal Brain Female	brain
21	chr2:96932800-96933400	Genic enhancers	Placenta	Placenta
22	chr2:96932800-96933400	Enhancers	Gastric	stomach
23	chr2:96932800-96933400	Weak transcription	Left Ventricle	heart
24	chr2:96932800-96933400	Enhancers	Ovary	ovary
25	chr2:96932800-96933600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:96932800-96933600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr2:96932800-96933600	Enhancers	Fetal Heart	heart
28	chr2:96932800-96933600	Enhancers	Psoas Muscle	Psoas
29	chr2:96932800-96933600	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr2:96932800-96933600	Genic enhancers	Thymus	Thymus
31	chr2:96932800-96933600	Transcr. at gene 5' and 3'	Dnd41	blood
32	chr2:96932800-96933800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:96932800-96934400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:96932800-96934800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:96932800-96970400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:96933000-96933400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:96933000-96933400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:96933000-96933400	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:96933000-96933400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:96933000-96933400	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
41	chr2:96933000-96933400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:96933000-96933400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:96933000-96933400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:96933000-96933400	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr2:96933000-96933400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
46	chr2:96933000-96933400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:96933000-96933400	Enhancers	Brain Angular Gyrus	brain
48	chr2:96933000-96933400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr2:96933000-96933400	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
50	chr2:96933000-96933400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach

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