Variant report

Variant	rs7428949
Chromosome Location	chr3:48545777-48545778
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48515040..48517957-chr3:48545083..48546816,2	MCF-7	breast:
2	chr3:48504031..48516338-chr3:48532689..48546353,31	MCF-7	breast:
3	chr3:48486688..48489552-chr3:48542310..48546358,4	K562	blood:
4	chr3:48545023..48546722-chr3:48547289..48549163,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TREX1-4	chr3:48544140-48547657	NONHSAT089581

Variant related genes	Relation type
ENSG00000164054	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000164053	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10049154	0.95[ASN][1000 genomes]
rs10470687	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11706983	1.00[JPT][hapmap]
rs11719291	1.00[JPT][hapmap]
rs11928552	1.00[JPT][hapmap]
rs12107252	1.00[JPT][hapmap]
rs12107418	1.00[JPT][hapmap]
rs12493578	1.00[JPT][hapmap]
rs13060933	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13062576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13063312	1.00[JPT][hapmap]
rs13064619	0.95[ASN][1000 genomes]
rs13070798	1.00[JPT][hapmap]
rs13091944	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13094578	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13100178	1.00[ASN][1000 genomes]
rs13319635	0.81[ASN][1000 genomes]
rs13319651	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13324142	1.00[JPT][hapmap]
rs13434258	1.00[JPT][hapmap]
rs17080319	1.00[JPT][hapmap]
rs2006871	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2276850	1.00[JPT][hapmap]
rs2276852	1.00[JPT][hapmap]
rs2286652	1.00[JPT][hapmap]
rs2302295	1.00[JPT][hapmap]
rs2310996	1.00[JPT][hapmap]
rs2854394	1.00[JPT][hapmap]
rs28563843	0.86[ASN][1000 genomes]
rs28881595	0.94[ASN][1000 genomes]
rs35064573	1.00[JPT][hapmap]
rs35562294	0.82[ASN][1000 genomes]
rs3755819	0.82[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	1.00[JPT][hapmap]
rs3821876	1.00[JPT][hapmap]
rs3969942	0.89[CHB][hapmap];1.00[ASN][1000 genomes]
rs4075082	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4858798	1.00[JPT][hapmap]
rs4858828	1.00[JPT][hapmap]
rs4858831	1.00[JPT][hapmap]
rs6442126	1.00[CHB][hapmap]
rs6442127	0.98[ASN][1000 genomes]
rs6765317	0.94[ASN][1000 genomes]
rs6773261	1.00[JPT][hapmap]
rs6781283	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6785845	0.95[ASN][1000 genomes]
rs6786424	0.82[ASN][1000 genomes]
rs6792156	1.00[JPT][hapmap]
rs6792525	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6806059	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6809981	0.95[ASN][1000 genomes]
rs740787	1.00[JPT][hapmap]
rs7434077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7434107	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620853	1.00[JPT][hapmap]
rs7623614	1.00[ASN][1000 genomes]
rs7631574	1.00[JPT][hapmap]
rs7640031	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644771	1.00[ASN][1000 genomes]
rs9810549	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9810991	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs9811027	1.00[JPT][hapmap]
rs9811318	1.00[JPT][hapmap]
rs9812200	1.00[JPT][hapmap]
rs9816942	1.00[ASN][1000 genomes]
rs9821797	1.00[JPT][hapmap]
rs9822677	0.95[ASN][1000 genomes]
rs9830581	1.00[JPT][hapmap]
rs9835827	0.95[ASN][1000 genomes]
rs9835902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9836462	1.00[JPT][hapmap]
rs9837687	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9841602	1.00[JPT][hapmap]
rs9843316	1.00[JPT][hapmap]
rs9848824	0.86[ASN][1000 genomes]
rs9849280	0.86[ASN][1000 genomes]
rs9850102	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9851743	1.00[ASN][1000 genomes]
rs9851771	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9864729	0.86[ASN][1000 genomes]
rs9869698	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9871180	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9871608	1.00[ASN][1000 genomes]
rs9873726	1.00[JPT][hapmap]
rs9875911	0.88[CHB][hapmap]
rs9878950	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9881877	0.82[ASN][1000 genomes]
rs9882962	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48542400-48545800	Enhancers	Primary T cells fromperipheralblood	blood
2	chr3:48542400-48545800	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr3:48542400-48545800	Enhancers	Placenta	Placenta
4	chr3:48542600-48554800	Weak transcription	Fetal Brain Female	brain
5	chr3:48542800-48554000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:48542800-48554800	Weak transcription	Brain Germinal Matrix	brain
7	chr3:48542800-48558200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:48542800-48562800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:48542800-48569800	Weak transcription	Right Atrium	heart
10	chr3:48543000-48549600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:48543000-48556000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:48543000-48556400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:48543000-48556600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:48543600-48545800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr3:48543600-48546200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:48544000-48561000	Weak transcription	K562	blood
17	chr3:48544200-48545800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr3:48544200-48545800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:48544200-48545800	Enhancers	HMEC	breast
20	chr3:48544200-48546200	Enhancers	Fetal Thymus	thymus
21	chr3:48544400-48545800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:48544600-48545800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr3:48544600-48545800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr3:48544800-48545800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:48544800-48546800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr3:48545000-48546600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:48545000-48546600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:48545000-48559800	Weak transcription	Fetal Intestine Large	intestine
29	chr3:48545200-48545800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:48545200-48546400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:48545200-48546400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:48545200-48546400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:48545200-48546600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:48545200-48558400	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:48545200-48558600	Weak transcription	NHLF	lung
36	chr3:48545200-48572400	Weak transcription	Brain Angular Gyrus	brain
37	chr3:48545400-48546400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr3:48545400-48546400	Weak transcription	Esophagus	oesophagus
39	chr3:48545400-48546800	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr3:48545400-48547200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:48545400-48554200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:48545400-48554200	Weak transcription	Fetal Intestine Small	intestine
43	chr3:48545400-48555600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:48545400-48555600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:48545400-48556000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:48545400-48556000	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:48545400-48556200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:48545400-48556400	Weak transcription	Brain Anterior Caudate	brain
49	chr3:48545400-48556600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:48545400-48556800	Weak transcription	Brain Substantia Nigra	brain

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