Variant report

Variant	rs10516289
Chromosome Location	chr4:15672200-15672201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:15663938..15667635-chr4:15670287..15673065,4	K562	blood:
2	chr4:15669222..15672294-chr4:15681695..15684873,3	K562	blood:
3	chr4:15653293..15659319-chr4:15668815..15673574,11	MCF-7	breast:
4	chr4:15655677..15658651-chr4:15671837..15675305,4	MCF-7	breast:
5	chr4:15664653..15666973-chr4:15669930..15673591,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118564	Chromatin interaction
ENSG00000237765	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10001565	0.90[CEU][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[ASN][1000 genomes]
rs10017222	1.00[CHB][hapmap]
rs11723554	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729955	1.00[CHB][hapmap]
rs11730336	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12643475	0.90[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12646913	0.90[CEU][hapmap];0.81[CHD][hapmap]
rs12650632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17405811	1.00[CHB][hapmap]
rs17406128	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17476642	1.00[CHB][hapmap]
rs1786	1.00[CHB][hapmap]
rs28532698	0.86[ASN][1000 genomes]
rs34910084	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3756247	1.00[CHB][hapmap]
rs4301111	1.00[CHB][hapmap]
rs4301112	0.92[ASN][1000 genomes]
rs4396986	1.00[CHB][hapmap]
rs4423870	1.00[CHB][hapmap]
rs4549375	1.00[CHB][hapmap]
rs56089642	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62290586	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62290588	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62290591	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62290593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62290595	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414764	1.00[CHB][hapmap]
rs6815254	1.00[CHB][hapmap]
rs6815296	1.00[CHB][hapmap]
rs6824422	1.00[CHB][hapmap]
rs6826058	1.00[CHB][hapmap]
rs6827406	1.00[CHB][hapmap]
rs6839654	1.00[CHB][hapmap]
rs6848779	1.00[CHB][hapmap]
rs73239201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7434484	1.00[CHB][hapmap]
rs7667512	0.90[CEU][hapmap]
rs7672311	0.90[CEU][hapmap];0.90[CHD][hapmap]
rs9942212	0.84[ASN][1000 genomes]
rs9994518	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv518830	chr4:15610771-15672200	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv3361772	chr4:15666732-15684418	Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10516289	TBC1D30	trans	lymphoblastoid	seeQTL
rs10516289	CD38	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15657600-15681400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:15658000-15672200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:15658000-15673800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:15658000-15675200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:15658000-15679000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:15658000-15681400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr4:15658200-15679200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:15658200-15679200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:15658200-15682200	Weak transcription	Fetal Stomach	stomach
10	chr4:15658600-15673000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:15658600-15679000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:15659800-15678600	Weak transcription	K562	blood
13	chr4:15660400-15679200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:15661600-15678600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:15662400-15678800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:15664800-15681800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:15667400-15675200	Weak transcription	Fetal Intestine Large	intestine
18	chr4:15667800-15673800	Weak transcription	Fetal Intestine Small	intestine
19	chr4:15668000-15676400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:15668200-15672600	Weak transcription	Placenta	Placenta
21	chr4:15668200-15678600	Weak transcription	NHLF	lung
22	chr4:15668400-15679000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:15668400-15682800	Weak transcription	Fetal Brain Male	brain
24	chr4:15668600-15673000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:15668600-15677000	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr4:15668600-15678800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:15668600-15679000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:15668600-15681400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:15668800-15678600	Weak transcription	Hela-S3	cervix
30	chr4:15669000-15677600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:15669000-15679000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:15669200-15672800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:15669400-15672800	Weak transcription	NH-A	brain
34	chr4:15669400-15673200	Weak transcription	A549	lung
35	chr4:15669400-15673800	Weak transcription	Fetal Thymus	thymus
36	chr4:15669400-15678600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr4:15669400-15678800	Weak transcription	Osteobl	bone
38	chr4:15669600-15673000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:15669600-15679000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:15669600-15679000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:15669600-15679000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:15669600-15681400	Weak transcription	Thymus	Thymus
43	chr4:15669800-15676600	Weak transcription	GM12878-XiMat	blood
44	chr4:15670000-15673000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr4:15670000-15673000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:15670000-15673000	Weak transcription	HMEC	breast
47	chr4:15670200-15672200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr4:15670200-15673000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:15670200-15673000	Weak transcription	NHEK	skin
50	chr4:15670800-15673400	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links