Variant report

Variant	rs13399261
Chromosome Location	chr2:48622918-48622919
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48620898..48623309-chr2:48624782..48626327,2	K562	blood:
2	chr2:48617829..48620871-chr2:48622412..48626412,3	K562	blood:
3	chr2:48130775..48133582-chr2:48622856..48624453,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138081	Chromatin interaction
ENSG00000233230	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10164456	1.00[AMR][1000 genomes]
rs10165262	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10167097	1.00[AMR][1000 genomes]
rs10168301	1.00[AMR][1000 genomes]
rs10169977	1.00[AMR][1000 genomes]
rs10170181	1.00[AMR][1000 genomes]
rs10177012	1.00[AMR][1000 genomes]
rs10178938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10180159	1.00[AMR][1000 genomes]
rs10183526	1.00[AMR][1000 genomes]
rs10184942	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10186155	1.00[AMR][1000 genomes]
rs10187019	1.00[AMR][1000 genomes]
rs10197056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10198245	1.00[AMR][1000 genomes]
rs10199098	1.00[AMR][1000 genomes]
rs10199615	1.00[AMR][1000 genomes]
rs10199764	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10200180	1.00[AMR][1000 genomes]
rs10204343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10206551	1.00[AMR][1000 genomes]
rs10208042	1.00[AMR][1000 genomes]
rs12328834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12329068	1.00[AMR][1000 genomes]
rs13390201	1.00[AMR][1000 genomes]
rs13391880	1.00[AMR][1000 genomes]
rs13396735	1.00[AMR][1000 genomes]
rs13402261	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13408747	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13410143	1.00[AMR][1000 genomes]
rs13418349	1.00[AMR][1000 genomes]
rs13419757	1.00[AFR][1000 genomes]
rs13422341	1.00[AMR][1000 genomes]
rs13424478	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13432235	1.00[AMR][1000 genomes]
rs28623311	1.00[AMR][1000 genomes]
rs28775335	1.00[AMR][1000 genomes]
rs28784960	1.00[AMR][1000 genomes]
rs28893847	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7340280	1.00[AMR][1000 genomes]
rs7355330	1.00[AMR][1000 genomes]
rs9653522	1.00[AMR][1000 genomes]
rs9653523	1.00[AMR][1000 genomes]
rs9653524	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48619200-48624600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:48619400-48623000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:48619400-48623000	Weak transcription	Fetal Intestine Large	intestine
4	chr2:48619400-48624000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:48619400-48624600	Weak transcription	Brain Angular Gyrus	brain
6	chr2:48619400-48624600	Weak transcription	Brain Anterior Caudate	brain
7	chr2:48619400-48624600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:48619400-48625400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:48619600-48624400	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:48621200-48623600	Weak transcription	Primary B cells from cord blood	blood
11	chr2:48622400-48623000	ZNF genes & repeats	Fetal Intestine Small	intestine
12	chr2:48622600-48623200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:48622600-48623400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:48622600-48623600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:48622600-48623600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr2:48622800-48623200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr2:48622800-48623200	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:48622800-48623200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:48622800-48623200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:48622800-48623200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:48622800-48623200	Enhancers	Adipose Nuclei	Adipose
22	chr2:48622800-48623200	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr2:48622800-48623200	Flanking Active TSS	Dnd41	blood
24	chr2:48622800-48623400	Enhancers	HepG2	liver
25	chr2:48622800-48623400	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr2:48622800-48623600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr2:48622800-48623600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr2:48622800-48623600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr2:48622800-48623600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr2:48622800-48623600	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr2:48622800-48623600	Enhancers	Duodenum Mucosa	Duodenum
32	chr2:48622800-48623600	Enhancers	Fetal Thymus	thymus
33	chr2:48622800-48623800	Enhancers	Primary T cells fromperipheralblood	blood
34	chr2:48622800-48623800	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr2:48622800-48623800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr2:48622800-48623800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:48622800-48624000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr2:48622800-48624200	Enhancers	Primary T cells from cord blood	blood

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