Variant report

Variant	rs242395
Chromosome Location	chr14:56599639-56599640
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56591173..56593665-chr14:56598218..56600855,2	MCF-7	breast:
2	chr14:56583354..56586083-chr14:56598668..56601939,3	K562	blood:

Variant related genes	Relation type
ENSG00000139946	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1028972	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1152473	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[EUR][1000 genomes]
rs1152474	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[MEX][hapmap];0.94[EUR][1000 genomes]
rs1152476	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[EUR][1000 genomes]
rs1152481	0.94[EUR][1000 genomes]
rs1479752	0.93[EUR][1000 genomes]
rs171411	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1979420	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[EUR][1000 genomes]
rs242385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs242393	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs242398	0.90[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs242406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs242407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs242410	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs242414	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs242417	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs242419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs242579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes]
rs242587	0.94[EUR][1000 genomes]
rs242588	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[EUR][1000 genomes]
rs242592	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.94[EUR][1000 genomes]
rs242593	0.94[EUR][1000 genomes]
rs242594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes]
rs34175054	0.94[EUR][1000 genomes]
rs375156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes]
rs3783668	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[EUR][1000 genomes]
rs402332	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs429676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.94[EUR][1000 genomes]
rs6573087	0.91[EUR][1000 genomes]
rs7140808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs7153057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs7153858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs753109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs754689	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.98[EUR][1000 genomes]
rs754690	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[EUR][1000 genomes]
rs899603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533129	chr14:56568535-56819234	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1844788	chr14:56594420-56771207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56592000-56601800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:56592400-56599800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr14:56592400-56600400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr14:56593200-56612800	Weak transcription	Brain Angular Gyrus	brain
5	chr14:56594600-56600600	Enhancers	Stomach Mucosa	stomach
6	chr14:56594600-56601400	Enhancers	Colon Smooth Muscle	Colon
7	chr14:56595000-56599800	Enhancers	Duodenum Mucosa	Duodenum
8	chr14:56595600-56607000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr14:56595800-56600600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr14:56596600-56600200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr14:56596600-56600200	Weak transcription	Esophagus	oesophagus
12	chr14:56596600-56600200	Weak transcription	Right Atrium	heart
13	chr14:56596600-56603600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr14:56596600-56615000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr14:56596800-56603600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr14:56596800-56604000	Weak transcription	Right Ventricle	heart
17	chr14:56596800-56604200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr14:56597000-56600200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr14:56597000-56600200	Weak transcription	Gastric	stomach
20	chr14:56597000-56600400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr14:56597000-56603400	Weak transcription	Spleen	Spleen
22	chr14:56597000-56611800	Weak transcription	Lung	lung
23	chr14:56597200-56600200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr14:56597200-56604000	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr14:56597200-56605600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr14:56597200-56607200	Enhancers	Dnd41	blood
27	chr14:56597400-56600800	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr14:56597600-56600400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr14:56597600-56600600	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr14:56597800-56600600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr14:56598200-56600400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr14:56598200-56600600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr14:56598200-56600600	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr14:56598200-56602000	Enhancers	Fetal Brain Male	brain
35	chr14:56598200-56606600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr14:56598400-56600200	Weak transcription	Thymus	Thymus
37	chr14:56598400-56604200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr14:56598800-56600600	Enhancers	H1 Cell Line	embryonic stem cell
39	chr14:56598800-56600600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr14:56598800-56601800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr14:56599000-56599800	Enhancers	H9 Cell Line	embryonic stem cell
42	chr14:56599000-56600200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr14:56599000-56600400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr14:56599000-56600600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr14:56599000-56600600	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr14:56599000-56604600	Weak transcription	Brain Anterior Caudate	brain
47	chr14:56599200-56600400	Weak transcription	Small Intestine	intestine
48	chr14:56599200-56602000	Weak transcription	Fetal Intestine Small	intestine
49	chr14:56599200-56603400	Weak transcription	Primary B cells from cord blood	blood
50	chr14:56599200-56604000	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links