Variant report

Variant	rs998242
Chromosome Location	chr14:64331334-64331335
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64319483..64322302-chr14:64328481..64332813,5	MCF-7	breast:
2	chr14:64319166..64320923-chr14:64328806..64331982,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000054654	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11158515	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11158518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11626911	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11628650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12161903	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12431956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12432760	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12435958	0.87[CHB][hapmap]
rs12586461	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12590842	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17750888	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17750906	0.93[ASN][1000 genomes]
rs1958413	0.84[JPT][hapmap]
rs2357001	0.87[CHB][hapmap]
rs4899121	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902253	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56376318	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56401218	0.80[ASN][1000 genomes]
rs60305436	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61985726	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61985748	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6573535	0.87[CHB][hapmap];0.80[ASN][1000 genomes]
rs66460676	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66764453	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67011590	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67106029	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67975797	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7140278	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7143794	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7145302	0.86[CHB][hapmap]
rs7145736	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7146469	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7149405	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73276854	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8008800	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8010312	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs8010385	0.92[ASN][1000 genomes]
rs8013611	0.91[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8016321	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8017009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs951249	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs951250	0.87[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1038825	chr14:64109441-64491720	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037140	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv542119	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64321200-64333800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:64321200-64334600	Weak transcription	Pancreas	Pancrea
3	chr14:64321200-64340600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr14:64321400-64350200	Weak transcription	Fetal Stomach	stomach
5	chr14:64322400-64334400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr14:64322800-64340400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr14:64322800-64340600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:64323000-64332800	Weak transcription	Fetal Intestine Small	intestine
9	chr14:64323000-64333000	Weak transcription	Ovary	ovary
10	chr14:64323200-64334400	Weak transcription	Aorta	Aorta
11	chr14:64323200-64340200	Weak transcription	Left Ventricle	heart
12	chr14:64323200-64340400	Weak transcription	Spleen	Spleen
13	chr14:64324600-64341400	Weak transcription	HSMM	muscle
14	chr14:64326800-64331600	Enhancers	Stomach Mucosa	stomach
15	chr14:64327000-64331400	Weak transcription	Thymus	Thymus
16	chr14:64327200-64332000	Weak transcription	Fetal Brain Female	brain
17	chr14:64327200-64340600	Weak transcription	Right Ventricle	heart
18	chr14:64327400-64333000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr14:64327400-64355200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr14:64327600-64360000	Weak transcription	Gastric	stomach
21	chr14:64327800-64334400	Weak transcription	Lung	lung
22	chr14:64327800-64342200	Weak transcription	Esophagus	oesophagus
23	chr14:64328400-64335000	Weak transcription	Psoas Muscle	Psoas
24	chr14:64328600-64331400	Flanking Active TSS	GM12878-XiMat	blood
25	chr14:64329000-64331600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr14:64329200-64334400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr14:64329600-64331400	Enhancers	Small Intestine	intestine
28	chr14:64330000-64331600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr14:64330200-64331600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr14:64330200-64343600	Weak transcription	Brain Germinal Matrix	brain
31	chr14:64330600-64331400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr14:64330600-64331400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr14:64330600-64331600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr14:64330600-64331600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr14:64330600-64331600	Enhancers	Liver	Liver
36	chr14:64330600-64331600	Enhancers	Fetal Thymus	thymus
37	chr14:64330600-64331600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr14:64330600-64331600	Flanking Active TSS	Dnd41	blood
39	chr14:64330600-64338200	Enhancers	Primary B cells from peripheral blood	blood
40	chr14:64330800-64331400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr14:64330800-64331600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr14:64330800-64331600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr14:64330800-64331600	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr14:64330800-64331600	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr14:64330800-64331600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr14:64330800-64331600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr14:64330800-64331600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr14:64330800-64331600	Enhancers	Muscle Satellite Cultured Cells	--
49	chr14:64330800-64331600	Enhancers	Adipose Nuclei	Adipose
50	chr14:64330800-64331600	Enhancers	Fetal Intestine Large	intestine

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