Variant report

Variant	rs3756083
Chromosome Location	chr4:147096213-147096214
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:147086830..147091007-chr4:147091903..147096779,4	K562	blood:
2	chr4:147096162..147099903-chr4:147161380..147165203,4	MCF-7	breast:
3	chr4:147095588..147099041-chr4:147101501..147104102,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251010	Chromatin interaction
ENSG00000164167	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10000407	0.80[AMR][1000 genomes]
rs10519776	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079476	0.98[ASN][1000 genomes]
rs11100919	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721367	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721873	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723069	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11724307	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11728525	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11728609	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11729787	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11730306	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11733347	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152657	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152692	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152709	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021106	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17021186	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021217	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17756234	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17757522	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757685	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17757715	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758092	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17758396	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17758420	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814023	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814065	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814503	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17814598	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865532	0.81[EUR][1000 genomes]
rs2007366	0.80[AMR][1000 genomes]
rs2068009	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115796	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115797	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163171	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164280	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28420466	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733458	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733459	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733460	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3756081	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756082	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775498	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815967	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4282199	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55736910	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56174047	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56279747	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56333123	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56393662	0.98[ASN][1000 genomes]
rs62326797	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62326801	0.94[ASN][1000 genomes]
rs62326802	0.94[ASN][1000 genomes]
rs62326804	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326848	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537400	0.80[AMR][1000 genomes]
rs6537401	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537402	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537403	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815527	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816161	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820462	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821066	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821444	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821479	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821863	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824313	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838458	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6839123	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6839141	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844381	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856647	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6858813	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72727944	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72727952	0.98[ASN][1000 genomes]
rs7657269	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665079	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695415	0.80[AMR][1000 genomes]
rs7745	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919482	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs919483	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461674	chr4:147047072-147143572	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv595650	chr4:147047072-147143572	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1018859	chr4:147055618-147138397	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3756083	RP11-6L6.2	cis	Whole Blood	GTEx
rs3756083	RP11-6L6.2	cis	Adipose Subcutaneous	GTEx
rs3756083	RP11-6L6.2	cis	Nerve Tibial	GTEx
rs3756083	RP11-6L6.2	cis	lung	GTEx
rs3756083	RP11-6L6.2	cis	Skin Sun Exposed Lower leg	GTEx
rs3756083	RP11-6L6.2	cis	Thyroid	GTEx
rs3756083	RP11-6L6.2	cis	Esophagus Muscularis	GTEx
rs3756083	RP11-6L6.2	cis	Artery Tibial	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147095200-147096600	Weak transcription	Ovary	ovary
2	chr4:147095400-147096400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr4:147095400-147096400	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr4:147096000-147096400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:147096200-147096400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:147096200-147096400	Enhancers	Primary B cells from cord blood	blood
7	chr4:147096200-147096400	Enhancers	Primary T cells from cord blood	blood
8	chr4:147096200-147096400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr4:147096200-147096400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr4:147096200-147096400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr4:147096200-147096400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:147096200-147096400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:147096200-147096400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:147096200-147096400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:147096200-147096400	Enhancers	Brain Angular Gyrus	brain
16	chr4:147096200-147096400	Enhancers	Brain Anterior Caudate	brain
17	chr4:147096200-147096400	Enhancers	A549	lung
18	chr4:147096200-147096400	Enhancers	GM12878-XiMat	blood
19	chr4:147096200-147096600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:147096200-147096600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr4:147096200-147096600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr4:147096200-147096600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr4:147096200-147096600	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr4:147096200-147096600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:147096200-147096800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:147096200-147096800	Flanking Active TSS	Dnd41	blood
27	chr4:147096200-147097200	Active TSS	HepG2	liver
28	chr4:147096200-147097400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:147096200-147098000	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr4:147096200-147098000	Active TSS	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links