Variant report

Variant	rs56839647
Chromosome Location	chr2:179279726-179279727
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:178974133..178981122-chr2:179276785..179281060,9	K562	blood:
2	chr2:179001333..179003104-chr2:179278827..179280728,2	MCF-7	breast:
3	chr2:179276988..179281129-chr2:179311895..179317764,7	MCF-7	breast:
4	chr2:178974532..178975128-chr2:179279107..179279741,2	MCF-7	breast:
5	chr2:179278797..179281186-chr2:180773348..180774954,2	K562	blood:
6	chr2:179278764..179281591-chr2:179306998..179309290,2	K562	blood:
7	chr2:179261404..179262451-chr2:179279050..179279981,4	K562	blood:
8	chr2:179270312..179272501-chr2:179279008..179282360,3	K562	blood:
9	chr2:179277180..179281325-chr2:179314213..179317479,5	K562	blood:
10	chr2:179170812..179171718-chr2:179279175..179279994,3	MCF-7	breast:
11	chr2:179238564..179240183-chr2:179278791..179280896,2	K562	blood:
12	chr2:178974519..178975080-chr2:179279294..179279980,2	MCF-7	breast:
13	chr2:179277322..179281063-chr2:179341771..179345640,5	K562	blood:
14	chr2:178771746..178772712-chr2:179279472..179279999,2	MCF-7	breast:
15	chr2:179278151..179280958-chr2:179342121..179344961,4	K562	blood:
16	chr2:179278754..179281325-chr2:179313064..179317479,4	K562	blood:
17	chr2:179261524..179262359-chr2:179279136..179280035,4	MCF-7	breast:
18	chr2:178997047..178997691-chr2:179278995..179280004,3	K562	blood:
19	chr2:179278648..179281403-chr2:179313491..179316018,3	MCF-7	breast:
20	chr2:179170847..179171754-chr2:179279256..179280544,7	MCF-7	breast:
21	chr2:178974707..178979925-chr2:179277151..179280371,6	K562	blood:
22	chr2:179278798..179282164-chr2:179284449..179287864,4	K562	blood:
23	chr2:179264734..179266660-chr2:179277060..179279815,2	MCF-7	breast:
24	chr2:178976618..178977561-chr2:179279109..179280071,3	K562	blood:
25	chr2:178976656..178977401-chr2:179279162..179279970,3	MCF-7	breast:
26	chr2:179279482..179281290-chr2:179287442..179289650,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000180228	Chromatin interaction
ENSG00000155636	Chromatin interaction
ENSG00000079150	Chromatin interaction
ENSG00000204311	Chromatin interaction
ENSG00000116095	Chromatin interaction
ENSG00000260931	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11893643	1.00[AMR][1000 genomes]
rs56986537	1.00[AMR][1000 genomes]
rs59265316	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034347	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034350	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034356	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034362	0.84[AFR][1000 genomes]
rs73034364	0.84[AFR][1000 genomes]
rs73034366	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034371	1.00[AMR][1000 genomes]
rs73034373	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73034375	1.00[AMR][1000 genomes]
rs73034393	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73036314	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73036316	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73036323	1.00[AMR][1000 genomes]
rs73036326	1.00[AMR][1000 genomes]
rs73036330	1.00[AMR][1000 genomes]
rs73036336	1.00[AMR][1000 genomes]
rs73036341	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv979349	chr2:179279539-179296355	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179277600-179280000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:179277600-179280000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:179277600-179280200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:179277600-179280400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:179277800-179279800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:179277800-179279800	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr2:179277800-179279800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr2:179277800-179279800	Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr2:179277800-179279800	Active TSS	Muscle Satellite Cultured Cells	--
10	chr2:179277800-179279800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:179277800-179279800	Active TSS	Brain Angular Gyrus	brain
12	chr2:179277800-179279800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:179277800-179279800	Active TSS	Rectal Smooth Muscle	rectum
14	chr2:179277800-179279800	Active TSS	Thymus	Thymus
15	chr2:179277800-179279800	Active TSS	GM12878-XiMat	blood
16	chr2:179277800-179280000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr2:179277800-179280000	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr2:179277800-179280000	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr2:179277800-179280000	Active TSS	Brain Anterior Caudate	brain
20	chr2:179277800-179280200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:179278000-179279800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:179278000-179279800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr2:179278000-179279800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:179278000-179279800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:179278000-179279800	Flanking Active TSS	Liver	Liver
26	chr2:179278000-179279800	Active TSS	Colon Smooth Muscle	Colon
27	chr2:179278000-179279800	Active TSS	Fetal Intestine Small	intestine
28	chr2:179278000-179279800	Active TSS	Left Ventricle	heart
29	chr2:179278000-179280000	Active TSS	H9 Cell Line	embryonic stem cell
30	chr2:179278000-179280000	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr2:179278000-179280000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr2:179278000-179280000	Active TSS	Brain Cingulate Gyrus	brain
33	chr2:179278200-179279800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr2:179278200-179279800	Active TSS	Fetal Brain Male	brain
35	chr2:179278200-179280000	Active TSS	Stomach Smooth Muscle	stomach
36	chr2:179278400-179279800	Active TSS	Brain Germinal Matrix	brain
37	chr2:179278400-179279800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr2:179278600-179279800	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr2:179278600-179279800	Active TSS	Fetal Muscle Trunk	muscle
40	chr2:179278800-179279800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr2:179278800-179279800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr2:179278800-179280000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:179278800-179280000	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr2:179278800-179280000	Flanking Active TSS	Fetal Brain Female	brain
45	chr2:179278800-179280000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr2:179278800-179291200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:179278800-179292800	Weak transcription	Spleen	Spleen
48	chr2:179278800-179293200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:179278800-179298800	Weak transcription	Small Intestine	intestine
50	chr2:179279000-179280000	Flanking Active TSS	NH-A	brain

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