Variant report

Variant	rs59227664
Chromosome Location	chr2:85866558-85866559
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:85866424-85866777	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:85860109..85864294-chr2:85864823..85868002,4	K562	blood:
2	chr2:85863255..85866624-chr2:85867202..85869540,4	K562	blood:
3	chr2:85864268..85866624-chr2:85868016..85871094,4	K562	blood:
4	chr2:85765276..85767700-chr2:85863355..85867135,3	MCF-7	breast:

Variant related genes	Relation type
USP39	TF binding region
ENSG00000168906	Chromatin interaction
ENSG00000168883	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs3024803	0.87[AMR][1000 genomes]
rs3024805	0.87[AMR][1000 genomes]
rs3024810	0.87[AMR][1000 genomes]
rs3024811	0.87[AMR][1000 genomes]
rs3024815	1.00[AMR][1000 genomes]
rs3024818	1.00[AMR][1000 genomes]
rs3024819	1.00[AMR][1000 genomes]
rs3024822	1.00[AMR][1000 genomes]
rs3024827	1.00[AMR][1000 genomes]
rs3024828	1.00[AMR][1000 genomes]
rs4416212	0.89[AFR][1000 genomes]
rs57175088	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57762218	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57789237	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs59048598	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59139634	0.86[AFR][1000 genomes]
rs60661938	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60755293	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60801683	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61535370	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61536745	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6718028	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923039	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923051	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923062	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923064	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923077	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923080	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923082	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7564769	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7579847	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7580358	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7584055	0.87[AMR][1000 genomes]
rs7589436	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7599812	0.96[AFR][1000 genomes];1.00[AMR][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	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874461	chr2:85853653-85939207	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv874462	chr2:85853653-85941074	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874463	chr2:85853653-85946708	Strong transcription Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv215431	chr2:85860999-85866615	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85843800-85876000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:85844800-85881600	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:85845000-85876000	Weak transcription	Right Atrium	heart
4	chr2:85845000-85879800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr2:85845000-85880000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:85845000-85880800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:85845000-85881400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:85845000-85881800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:85845000-85883600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:85845400-85879800	Strong transcription	Lung	lung
11	chr2:85845400-85881000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:85845400-85881400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:85845400-85886400	Strong transcription	Fetal Muscle Leg	muscle
14	chr2:85845600-85881800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:85845600-85882200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr2:85845800-85881400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:85845800-85881600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:85845800-85881800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:85846000-85875600	Strong transcription	Primary hematopoietic stem cells	blood
20	chr2:85846000-85880800	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:85846000-85881400	Strong transcription	Fetal Stomach	stomach
22	chr2:85846000-85881400	Strong transcription	Fetal Thymus	thymus
23	chr2:85846000-85887000	Strong transcription	Liver	Liver
24	chr2:85846000-85887400	Strong transcription	Fetal Intestine Small	intestine
25	chr2:85846200-85871600	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:85846200-85874600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:85846200-85874600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr2:85846200-85875000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:85846200-85875200	Strong transcription	Placenta	Placenta
30	chr2:85846200-85879400	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:85846200-85879400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:85846200-85880000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:85846200-85880000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:85846200-85880000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr2:85846200-85880600	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr2:85846200-85881200	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:85846200-85881400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:85846200-85881400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:85846200-85882000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:85846200-85889400	Strong transcription	Thymus	Thymus
41	chr2:85846400-85869200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:85846400-85879600	Strong transcription	Fetal Intestine Large	intestine
43	chr2:85846400-85880600	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr2:85846600-85869400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:85846600-85875600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr2:85846800-85881400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr2:85846800-85881600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:85847000-85875000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:85847000-85876200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:85847600-85880000	Strong transcription	Fetal Lung	lung

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