Variant report

Variant	rs7564769
Chromosome Location	chr2:85856620-85856621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85856113..85858844-chr2:85885190..85887112,2	MCF-7	breast:
2	chr2:85851675..85853716-chr2:85856128..85857675,2	MCF-7	breast:
3	chr2:85764659..85766250-chr2:85854186..85857174,2	MCF-7	breast:
4	chr2:85855008..85857612-chr2:85860725..85862403,3	MCF-7	breast:
5	chr2:85850244..85853490-chr2:85856097..85860069,4	K562	blood:
6	chr2:85847247..85848767-chr2:85853795..85856664,2	K562	blood:

Variant related genes	Relation type
ENSG00000168883	Chromatin interaction

Extended variants
information (count: 40 )
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[MEX][hapmap];0.83[MKK][hapmap];1.00[AMR][1000 genomes]
rs3024818	1.00[AMR][1000 genomes]
rs3024819	1.00[AMR][1000 genomes]
rs3024822	1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[AMR][1000 genomes]
rs3024827	1.00[AMR][1000 genomes]
rs3024828	1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[AMR][1000 genomes]
rs4416212	0.89[AFR][1000 genomes]
rs57175088	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57762218	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57789237	0.87[AMR][1000 genomes]
rs59048598	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59139634	0.88[AFR][1000 genomes]
rs59227664	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60661938	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60755293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60801683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61535370	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61536745	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6718028	0.87[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923039	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923051	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923062	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923064	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923077	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923080	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923082	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7579847	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7580358	0.93[ASW][hapmap];0.87[LWK][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes]
rs7584055	0.87[AMR][1000 genomes]
rs7589436	0.87[AMR][1000 genomes]
rs7599812	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][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	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

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	chr2:85844800-85858400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:85844800-85862600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:85844800-85881600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:85845000-85876000	Weak transcription	Right Atrium	heart
6	chr2:85845000-85879800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:85845000-85880000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:85845000-85880800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:85845000-85881400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:85845000-85881800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:85845000-85883600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:85845400-85864600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:85845400-85879800	Strong transcription	Lung	lung
14	chr2:85845400-85881000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:85845400-85881400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:85845400-85886400	Strong transcription	Fetal Muscle Leg	muscle
17	chr2:85845600-85881800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:85845600-85882200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr2:85845800-85860800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:85845800-85865000	Strong transcription	NH-A	brain
21	chr2:85845800-85881400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:85845800-85881600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:85845800-85881800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:85846000-85875600	Strong transcription	Primary hematopoietic stem cells	blood
25	chr2:85846000-85880800	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:85846000-85881400	Strong transcription	Fetal Stomach	stomach
27	chr2:85846000-85881400	Strong transcription	Fetal Thymus	thymus
28	chr2:85846000-85887000	Strong transcription	Liver	Liver
29	chr2:85846000-85887400	Strong transcription	Fetal Intestine Small	intestine
30	chr2:85846200-85864200	Strong transcription	Brain Germinal Matrix	brain
31	chr2:85846200-85871600	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:85846200-85874600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr2:85846200-85874600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr2:85846200-85875000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:85846200-85875200	Strong transcription	Placenta	Placenta
36	chr2:85846200-85879400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:85846200-85879400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:85846200-85880000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:85846200-85880000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:85846200-85880000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr2:85846200-85880600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr2:85846200-85881200	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr2:85846200-85881400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:85846200-85881400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:85846200-85882000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:85846200-85889400	Strong transcription	Thymus	Thymus
47	chr2:85846400-85864600	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr2:85846400-85864800	Strong transcription	Primary B cells from cord blood	blood
49	chr2:85846400-85869200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:85846400-85879600	Strong transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links