Variant report

Variant	rs2540895
Chromosome Location	chr14:77649021-77649022
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:77606589..77609950-chr14:77648751..77652223,3	MCF-7	breast:
2	chr14:77640676..77643134-chr14:77646615..77650592,3	MCF-7	breast:
3	chr14:77646733..77650700-chr14:77767687..77771144,4	MCF-7	breast:
4	chr14:77647339..77650955-chr14:77785389..77788358,5	MCF-7	breast:
5	chr14:77646577..77649681-chr14:77786771..77790034,4	MCF-7	breast:
6	chr14:77635396..77638005-chr14:77648912..77652690,3	MCF-7	breast:
7	chr14:77648085..77652144-chr14:77770230..77773335,4	MCF-7	breast:
8	chr14:77562647..77564401-chr14:77648231..77649984,2	MCF-7	breast:
9	chr14:77642180..77644687-chr14:77647056..77649855,2	MCF-7	breast:
10	chr14:77648815..77651444-chr14:77730169..77732622,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000100577	Chromatin interaction
ENSG00000165548	Chromatin interaction
ENSG00000221754	Chromatin interaction
ENSG00000177108	Chromatin interaction
ENSG00000009830	Chromatin interaction
ENSG00000269883	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10143567	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1504522	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17105476	0.91[ASN][1000 genomes]
rs17750140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2021536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2287380	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes]
rs2540887	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs2540891	0.89[EUR][1000 genomes]
rs2540893	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2540894	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2540901	0.91[CEU][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2655976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2655977	0.89[EUR][1000 genomes]
rs34002218	0.89[EUR][1000 genomes]
rs34970502	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs367095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs374227	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs376645	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs380489	1.00[CHB][hapmap]
rs382670	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs382868	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs384204	1.00[CHB][hapmap]
rs396750	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs404418	1.00[AFR][1000 genomes]
rs419630	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[AFR][1000 genomes]
rs419869	1.00[AFR][1000 genomes]
rs428868	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs451303	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4903561	1.00[CEU][hapmap]
rs71413450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs750932	0.90[CEU][hapmap];1.00[AMR][1000 genomes]
rs8010477	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes]
rs905734	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs905735	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][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	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription 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 miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv832834	chr14:77554987-77724357	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv976845	chr14:77621865-77649191	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2540895	ACCN2	cis	Temporal Cortex	GTEx
rs2540895	TMEM63C	cis	Whole Blood	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77647600-77649200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr14:77647600-77649200	Enhancers	Spleen	Spleen
3	chr14:77647600-77649400	Active TSS	Brain Anterior Caudate	brain
4	chr14:77647800-77649200	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr14:77647800-77649200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr14:77647800-77649200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
7	chr14:77647800-77649200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr14:77647800-77650000	Active TSS	Brain Angular Gyrus	brain
9	chr14:77648000-77649400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
10	chr14:77648000-77650000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr14:77648200-77649400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
12	chr14:77648400-77649200	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr14:77648400-77649200	Flanking Active TSS	Fetal Intestine Small	intestine
14	chr14:77648400-77649200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr14:77648400-77649200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
16	chr14:77648600-77649200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr14:77648600-77649200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr14:77648600-77649400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr14:77648600-77649600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr14:77648600-77650400	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr14:77648600-77650600	Weak transcription	Gastric	stomach
22	chr14:77648600-77653000	Weak transcription	Fetal Heart	heart
23	chr14:77648800-77649200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr14:77648800-77649200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr14:77648800-77649200	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr14:77648800-77649200	Bivalent Enhancer	Placenta	Placenta
27	chr14:77648800-77649200	Bivalent Enhancer	Fetal Thymus	thymus
28	chr14:77648800-77649600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr14:77648800-77649600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
30	chr14:77648800-77649800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr14:77648800-77650000	Enhancers	Brain Substantia Nigra	brain
32	chr14:77648800-77650600	Enhancers	Fetal Brain Male	brain
33	chr14:77648800-77650800	Bivalent Enhancer	Fetal Muscle Leg	muscle
34	chr14:77648800-77650800	Weak transcription	NHEK	skin
35	chr14:77648800-77653200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr14:77648800-77654800	Weak transcription	Right Atrium	heart
37	chr14:77649000-77649200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
38	chr14:77649000-77649200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
39	chr14:77649000-77649200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr14:77649000-77649200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr14:77649000-77649200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
42	chr14:77649000-77649200	Bivalent Enhancer	Fetal Intestine Large	intestine
43	chr14:77649000-77649400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
44	chr14:77649000-77649400	Bivalent Enhancer	Primary T cells from cord blood	blood
45	chr14:77649000-77649400	Enhancers	Primary hematopoietic stem cells	blood
46	chr14:77649000-77649400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr14:77649000-77649400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr14:77649000-77649400	Enhancers	Esophagus	oesophagus
49	chr14:77649000-77649400	Flanking Active TSS	Fetal Brain Female	brain
50	chr14:77649000-77649400	Enhancers	HMEC	breast

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