Variant report

Variant	rs56129857
Chromosome Location	chr2:97576523-97576524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97559950..97563991-chr2:97572149..97576823,4	K562	blood:
2	chr2:97569777..97572197-chr2:97574930..97577007,2	K562	blood:
3	chr2:97560120..97562357-chr2:97575794..97577324,2	K562	blood:
4	chr2:97575476..97578400-chr2:97584018..97588039,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1047634	1.00[EUR][1000 genomes]
rs11886360	1.00[EUR][1000 genomes]
rs11892821	1.00[EUR][1000 genomes]
rs2314649	1.00[EUR][1000 genomes]
rs34013660	1.00[EUR][1000 genomes]
rs57184334	1.00[EUR][1000 genomes]
rs58448521	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6576985	1.00[EUR][1000 genomes]
rs6576988	1.00[EUR][1000 genomes]
rs6576991	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6707008	1.00[EUR][1000 genomes]
rs6733535	1.00[EUR][1000 genomes]
rs6733826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6744498	1.00[EUR][1000 genomes]
rs6746421	1.00[EUR][1000 genomes]
rs6748214	1.00[EUR][1000 genomes]
rs6748234	1.00[EUR][1000 genomes]
rs6759613	1.00[EUR][1000 genomes]
rs72945119	1.00[EUR][1000 genomes]
rs72947013	1.00[EUR][1000 genomes]
rs73960684	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73960686	1.00[AMR][1000 genomes]
rs7580104	1.00[EUR][1000 genomes]
rs7587149	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers 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	55 gene(s)	inside rSNPs	diseases
10	nsv582497	chr2:97569305-97715154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 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	chr2:97572400-97579200	Enhancers	Fetal Brain Male	brain
2	chr2:97573200-97578000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:97573600-97577800	Weak transcription	K562	blood
4	chr2:97573600-97578000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:97573800-97577600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:97573800-97577600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:97573800-97579000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:97574000-97577200	Weak transcription	Brain Germinal Matrix	brain
9	chr2:97574000-97577400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:97574000-97578000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:97574000-97578000	Weak transcription	Lung	lung
12	chr2:97574000-97578200	Weak transcription	Esophagus	oesophagus
13	chr2:97574000-97578200	Weak transcription	Fetal Thymus	thymus
14	chr2:97574000-97578600	Weak transcription	Placenta	Placenta
15	chr2:97574000-97582000	Weak transcription	Colonic Mucosa	Colon
16	chr2:97574200-97577600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:97574200-97577800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:97574200-97578200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:97574200-97578400	Weak transcription	Pancreas	Pancrea
20	chr2:97574800-97577200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr2:97575000-97576600	Enhancers	Fetal Brain Female	brain
22	chr2:97575200-97576800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:97575200-97577400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:97575400-97576800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr2:97575400-97577000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:97575400-97577600	Weak transcription	Primary T cells from cord blood	blood
27	chr2:97575400-97577800	Weak transcription	Adipose Nuclei	Adipose
28	chr2:97575400-97579200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:97575600-97577000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:97575600-97577200	Enhancers	Fetal Heart	heart
31	chr2:97575600-97581600	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:97575800-97577000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:97575800-97577000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:97575800-97577200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:97575800-97577400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr2:97575800-97577600	Weak transcription	Brain Anterior Caudate	brain
37	chr2:97575800-97577600	Weak transcription	Spleen	Spleen
38	chr2:97575800-97578600	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:97575800-97581800	Weak transcription	Right Atrium	heart
40	chr2:97576000-97576800	Weak transcription	Brain Angular Gyrus	brain
41	chr2:97576000-97577000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:97576000-97577000	Weak transcription	Right Ventricle	heart
43	chr2:97576000-97578800	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr2:97576000-97581600	Weak transcription	Brain Substantia Nigra	brain
45	chr2:97576200-97576800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:97576200-97577000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:97576200-97578200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:97576400-97576800	Weak transcription	Left Ventricle	heart
49	chr2:97576400-97578200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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