Variant report

Variant	rs4286259
Chromosome Location	chr2:62732614-62732615
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:62732196..62734647-chr2:62932204..62934327,2	K562	blood:
2	chr2:62730535..62732862-chr2:62735147..62737485,2	K562	blood:
3	chr2:62706782..62709578-chr2:62731639..62733340,2	K562	blood:
4	chr2:62732443..62734653-chr2:62900758..62903078,2	MCF-7	breast:
5	chr2:62730719..62734296-chr2:62930912..62935708,9	MCF-7	breast:
6	chr2:62731472..62734976-chr2:62932827..62936526,3	K562	blood:
7	chr2:62731742..62734497-chr2:62931519..62934102,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115504	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10191324	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10191428	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11125927	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11903221	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13035295	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13388903	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13389363	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13396048	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4233979	0.84[CEU][hapmap]
rs4405748	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4672527	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4672528	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57645001	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6745280	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6757222	0.93[ASN][1000 genomes]
rs6757448	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs73934251	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73934252	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73934253	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7582882	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7604354	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv2751	chr2:62691264-62737131	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62719600-62732800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:62729800-62733200	Weak transcription	HepG2	liver
3	chr2:62732200-62732800	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr2:62732200-62732800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:62732200-62732800	Enhancers	Stomach Mucosa	stomach
6	chr2:62732200-62732800	Flanking Active TSS	A549	lung
7	chr2:62732200-62732800	Enhancers	HUVEC	blood vessel
8	chr2:62732200-62732800	Enhancers	NH-A	brain
9	chr2:62732200-62732800	Enhancers	NHLF	lung
10	chr2:62732200-62733600	Active TSS	Primary B cells from cord blood	blood
11	chr2:62732200-62733800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:62732200-62733800	Active TSS	Brain Cingulate Gyrus	brain
13	chr2:62732400-62732800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:62732400-62732800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:62732400-62732800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:62732400-62732800	Enhancers	Primary B cells from peripheral blood	blood
17	chr2:62732400-62732800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr2:62732400-62732800	Enhancers	Fetal Brain Male	brain
19	chr2:62732400-62732800	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr2:62732400-62732800	Enhancers	Small Intestine	intestine
21	chr2:62732400-62732800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr2:62732400-62733000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:62732400-62733000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:62732400-62733600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:62732400-62733600	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr2:62732400-62733600	Active TSS	Stomach Smooth Muscle	stomach
27	chr2:62732400-62733800	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr2:62732400-62733800	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr2:62732400-62733800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:62732400-62733800	Active TSS	Brain Angular Gyrus	brain
31	chr2:62732400-62733800	Active TSS	Colonic Mucosa	Colon
32	chr2:62732400-62733800	Active TSS	Duodenum Mucosa	Duodenum
33	chr2:62732400-62733800	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr2:62732400-62733800	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr2:62732400-62733800	Active TSS	GM12878-XiMat	blood
36	chr2:62732400-62734000	Active TSS	H1 Cell Line	embryonic stem cell
37	chr2:62732400-62734000	Active TSS	Brain Substantia Nigra	brain
38	chr2:62732400-62734000	Active TSS	Fetal Brain Female	brain
39	chr2:62732400-62734000	Active TSS	Fetal Kidney	kidney
40	chr2:62732400-62734000	Active TSS	Fetal Thymus	thymus
41	chr2:62732600-62732800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr2:62732600-62732800	Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr2:62732600-62732800	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr2:62732600-62732800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:62732600-62732800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:62732600-62732800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:62732600-62732800	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr2:62732600-62732800	Active TSS	Right Atrium	heart
49	chr2:62732600-62732800	Active TSS	Thymus	Thymus
50	chr2:62732600-62732800	Enhancers	HMEC	breast

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