Variant report

Variant	rs6882235
Chromosome Location	chr5:50260139-50260140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:38003355..38005334-chr5:50260049..50263278,3	MCF-7	breast:
2	chr5:50252384..50255461-chr5:50257528..50260468,3	K562	blood:

Variant related genes	Relation type
ENSG00000100083	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10035173	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10054150	0.81[AMR][1000 genomes]
rs11746939	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1345777	0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs151986	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs151997	0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs152817	0.85[YRI][hapmap]
rs250230	1.00[YRI][hapmap]
rs27247	0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs27249	0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3846498	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3846499	0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3846500	0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62367393	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6870880	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9292165	0.94[AFR][1000 genomes];0.92[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	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv830286	chr5:50165805-50374600	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50258600-50261600	Active TSS	Stomach Smooth Muscle	stomach
2	chr5:50258600-50266600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr5:50258800-50260200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:50258800-50260200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
5	chr5:50258800-50260400	Active TSS	Right Atrium	heart
6	chr5:50259000-50260200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr5:50259000-50260200	Bivalent/Poised TSS	Colonic Mucosa	Colon
8	chr5:50259000-50260400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:50259000-50260400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:50259000-50260400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr5:50259000-50260400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr5:50259000-50260400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
13	chr5:50259000-50260400	Enhancers	Lung	lung
14	chr5:50259000-50260400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
15	chr5:50259000-50260600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr5:50259200-50260200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:50259200-50260400	Bivalent/Poised TSS	Primary B cells from cord blood	blood
18	chr5:50259400-50260200	Enhancers	Spleen	Spleen
19	chr5:50259400-50260400	Bivalent Enhancer	Fetal Heart	heart
20	chr5:50259400-50260400	Bivalent Enhancer	Fetal Lung	lung
21	chr5:50259400-50260400	Enhancers	Pancreas	Pancrea
22	chr5:50259600-50260200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
23	chr5:50259600-50260200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
24	chr5:50259600-50260200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
25	chr5:50259600-50260200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
26	chr5:50259600-50260200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:50259600-50260200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
28	chr5:50259600-50260200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:50259600-50260200	Bivalent Enhancer	Placenta	Placenta
30	chr5:50259600-50260200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
31	chr5:50259600-50260400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
32	chr5:50259600-50260400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
33	chr5:50259600-50260400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
34	chr5:50259600-50260400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:50259600-50260400	Bivalent Enhancer	Liver	Liver
36	chr5:50259600-50260400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr5:50259600-50260400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr5:50259600-50260400	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr5:50259600-50260600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:50259600-50260600	Bivalent Enhancer	Fetal Brain Male	brain
41	chr5:50259600-50260600	Bivalent Enhancer	Fetal Intestine Small	intestine
42	chr5:50259600-50260800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
43	chr5:50259600-50260800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
44	chr5:50259800-50260200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:50259800-50260200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
46	chr5:50259800-50260200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
47	chr5:50259800-50260200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:50259800-50260200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
49	chr5:50259800-50260200	Bivalent Enhancer	Right Ventricle	heart
50	chr5:50259800-50260400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell

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