Variant report

Variant	rs2440982
Chromosome Location	chr5:14279540-14279541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14273020..14274776-chr5:14278391..14281158,2	MCF-7	breast:
2	chr5:14279019..14280717-chr5:14281044..14283924,2	K562	blood:
3	chr5:14107611..14110388-chr5:14277452..14281941,4	MCF-7	breast:
4	chr5:14143194..14145059-chr5:14276873..14279594,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12522960	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs154150	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs164859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs164860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs164862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs164863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs165092	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs165094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs165095	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs165096	0.87[ASN][1000 genomes]
rs16903338	0.90[JPT][hapmap]
rs26281	0.83[MEX][hapmap]
rs30618	0.82[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs30621	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs30626	0.91[ASN][1000 genomes]
rs30627	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30628	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30629	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs30630	0.92[ASN][1000 genomes]
rs30631	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs30632	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs30633	0.82[CHB][hapmap]
rs30635	0.84[ASN][1000 genomes]
rs32571	0.83[MEX][hapmap]
rs354303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs356026	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs356027	0.92[ASN][1000 genomes]
rs356028	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356029	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs42253	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4701604	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56334634	0.87[ASN][1000 genomes]
rs58221971	0.85[ASN][1000 genomes]
rs6554849	0.85[ASN][1000 genomes]
rs6554850	0.87[ASN][1000 genomes]
rs6554851	0.87[ASN][1000 genomes]
rs7380307	0.82[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7700787	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]

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	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14265200-14293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:14265400-14284600	Weak transcription	Stomach Mucosa	stomach
3	chr5:14265400-14286600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:14268600-14291000	Weak transcription	Fetal Kidney	kidney
5	chr5:14269200-14280000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:14269200-14286400	Weak transcription	Pancreas	Pancrea
7	chr5:14269200-14286600	Weak transcription	Spleen	Spleen
8	chr5:14270200-14290800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:14270400-14279800	Weak transcription	Ovary	ovary
10	chr5:14270400-14280400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:14270400-14280400	Weak transcription	Placenta	Placenta
12	chr5:14270400-14280400	Weak transcription	Fetal Thymus	thymus
13	chr5:14270400-14280600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr5:14270400-14280600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:14270400-14280600	Weak transcription	Lung	lung
16	chr5:14270400-14283200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:14270400-14284400	Weak transcription	Colonic Mucosa	Colon
18	chr5:14270400-14284600	Weak transcription	Brain Germinal Matrix	brain
19	chr5:14270400-14284800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:14270400-14284800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:14270400-14286400	Weak transcription	Fetal Intestine Small	intestine
22	chr5:14270400-14286800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr5:14270400-14288800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr5:14270400-14289400	Weak transcription	Gastric	stomach
25	chr5:14270400-14293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:14270400-14305200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:14270400-14313600	Weak transcription	Small Intestine	intestine
28	chr5:14270600-14279800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:14270800-14279800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:14270800-14280200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:14270800-14280200	Weak transcription	Fetal Lung	lung
32	chr5:14270800-14280200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr5:14270800-14280400	Weak transcription	Fetal Muscle Leg	muscle
34	chr5:14270800-14280600	Weak transcription	Fetal Intestine Large	intestine
35	chr5:14270800-14281400	Weak transcription	Fetal Stomach	stomach
36	chr5:14270800-14282000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr5:14270800-14286800	Weak transcription	Fetal Brain Male	brain
38	chr5:14270800-14293000	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:14271000-14280400	Weak transcription	Adipose Nuclei	Adipose
40	chr5:14271000-14295800	Weak transcription	Brain Angular Gyrus	brain
41	chr5:14271800-14280200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:14271800-14280600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:14271800-14284400	Weak transcription	Aorta	Aorta
44	chr5:14272200-14280400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr5:14272200-14281600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:14272400-14279600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:14272400-14279600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr5:14272400-14280200	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr5:14272400-14280400	Weak transcription	Liver	Liver
50	chr5:14272400-14280400	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links