Variant report

Variant	rs4558636
Chromosome Location	chr2:47538581-47538582
allele	C/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:47398263..47400819-chr2:47535902..47539310,3	MCF-7	breast:
2	chr2:47497085..47500611-chr2:47536768..47542000,5	MCF-7	breast:
3	chr2:47400906..47404753-chr2:47537729..47542393,7	K562	blood:
4	chr2:47484907..47487691-chr2:47537998..47540453,2	MCF-7	breast:
5	chr2:47527356..47529595-chr2:47537619..47539608,2	K562	blood:
6	chr2:47402318..47405024-chr2:47536306..47539127,3	MCF-7	breast:
7	chr2:47385656..47388232-chr2:47538182..47540860,2	MCF-7	breast:
8	chr2:47395267..47408439-chr2:47533772..47553038,55	MCF-7	breast:
9	chr2:47398506..47400133-chr2:47537850..47540802,2	K562	blood:
10	chr2:47400534..47404753-chr2:47537729..47541997,7	K562	blood:
11	chr2:47498345..47500843-chr2:47537583..47540511,2	MCF-7	breast:
12	chr2:47536098..47538713-chr2:47547950..47550505,2	MCF-7	breast:
13	chr2:47424415..47427832-chr2:47536667..47539203,3	MCF-7	breast:
14	chr2:47529427..47534518-chr2:47538025..47540772,4	MCF-7	breast:
15	chr2:47500714..47503481-chr2:47536098..47539031,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10168995	0.81[CHB][hapmap]
rs10180711	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10192326	0.89[CHB][hapmap]
rs12471906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4560164	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6544977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544978	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6720211	0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6734711	0.81[CHB][hapmap]
rs9789479	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9789683	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	50 gene(s)	inside rSNPs	diseases
4	nsv457385	chr2:47468331-47552277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv581755	chr2:47468331-47552277	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47520800-47540000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:47530400-47541200	Enhancers	Fetal Intestine Small	intestine
3	chr2:47530400-47541600	Enhancers	Fetal Intestine Large	intestine
4	chr2:47534400-47550400	Weak transcription	Ovary	ovary
5	chr2:47535000-47538800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:47535000-47540600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:47536200-47539400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:47536200-47540000	Enhancers	Primary B cells from peripheral blood	blood
9	chr2:47536200-47541400	Enhancers	Stomach Mucosa	stomach
10	chr2:47536400-47538600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
11	chr2:47536400-47538600	Flanking Active TSS	HepG2	liver
12	chr2:47536400-47539000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:47536600-47538800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:47536600-47539000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr2:47536600-47539600	Enhancers	Placenta	Placenta
16	chr2:47536600-47541000	Enhancers	Primary hematopoietic stem cells	blood
17	chr2:47536800-47538600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:47536800-47538600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:47536800-47538600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:47536800-47538600	Enhancers	Fetal Lung	lung
21	chr2:47536800-47538600	Enhancers	Fetal Thymus	thymus
22	chr2:47536800-47538600	Enhancers	Hela-S3	cervix
23	chr2:47536800-47538600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr2:47536800-47538800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:47536800-47538800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:47536800-47538800	Enhancers	Adipose Nuclei	Adipose
27	chr2:47536800-47538800	Flanking Active TSS	Brain Hippocampus Middle	brain
28	chr2:47536800-47538800	Enhancers	Fetal Heart	heart
29	chr2:47536800-47538800	Enhancers	Psoas Muscle	Psoas
30	chr2:47536800-47538800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr2:47536800-47538800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr2:47536800-47538800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:47536800-47538800	Enhancers	Thymus	Thymus
34	chr2:47536800-47538800	Enhancers	Spleen	Spleen
35	chr2:47536800-47539000	Enhancers	Brain Germinal Matrix	brain
36	chr2:47536800-47539200	Enhancers	Right Atrium	heart
37	chr2:47537000-47538600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:47537000-47538600	Enhancers	Fetal Muscle Leg	muscle
39	chr2:47537000-47538600	Enhancers	NH-A	brain
40	chr2:47537000-47538800	Enhancers	Colon Smooth Muscle	Colon
41	chr2:47537000-47538800	Enhancers	Left Ventricle	heart
42	chr2:47537200-47538600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:47537200-47538600	Enhancers	Fetal Stomach	stomach
44	chr2:47537200-47538800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:47537200-47538800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:47537200-47538800	Enhancers	Pancreas	Pancrea
47	chr2:47537200-47538800	Enhancers	Rectal Smooth Muscle	rectum
48	chr2:47537400-47538600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr2:47537400-47538600	Enhancers	Fetal Muscle Trunk	muscle
50	chr2:47537400-47538800	Flanking Active TSS	Duodenum Mucosa	Duodenum

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