Variant report

Variant	rs2624848
Chromosome Location	chr3:50165101-50165102
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50164743..50166299-chr3:50183403..50185616,2	MCF-7	breast:
2	chr3:50157879..50160528-chr3:50162974..50166130,4	K562	blood:
3	chr3:50164220..50165841-chr3:50169417..50171104,2	MCF-7	breast:
4	chr3:50157840..50167526-chr3:50182100..50196634,43	MCF-7	breast:
5	chr3:50164983..50167115-chr3:50208238..50210374,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000001617	Chromatin interaction
ENSG00000235016	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1061474	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1138536	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12107768	0.88[ASN][1000 genomes]
rs2240328	0.91[ASN][1000 genomes]
rs2247510	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2526747	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2526749	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526750	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2624815	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2624817	0.91[ASN][1000 genomes]
rs2624822	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2624826	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2624829	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2624834	0.91[ASN][1000 genomes]
rs2856237	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2856238	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3774734	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688753	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4688754	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6446194	0.84[ASN][1000 genomes]
rs6446195	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6446197	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6762477	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6793528	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6799579	0.88[ASN][1000 genomes]
rs6808044	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7061	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7430334	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7634441	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9682295	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv818139	chr3:50144951-50174572	Weak transcription Strong transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
8	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
11	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
12	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
13	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
14	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
15	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
16	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2624848	RBM6	cis	Artery Tibial	GTEx
rs2624848	RBM6	cis	Whole Blood	GTEx
rs2624848	RBM6	cis	Esophagus Mucosa	GTEx
rs2624848	RBM6	cis	Artery Aorta	GTEx
rs2624848	RBM6	cis	Nerve Tibial	GTEx
rs2624848	RBM6	cis	Heart Left Ventricle	GTEx
rs2624848	RBM6	cis	Esophagus Muscularis	GTEx
rs2624848	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2624848	RBM6	cis	Adipose Subcutaneous	GTEx
rs2624848	RBM6	cis	Thyroid	GTEx
rs2624848	RBM6	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50151000-50176400	Weak transcription	Right Atrium	heart
2	chr3:50159200-50165200	Enhancers	Fetal Lung	lung
3	chr3:50159800-50168600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr3:50161400-50165200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:50161400-50165200	Enhancers	Lung	lung
6	chr3:50161400-50165200	Enhancers	Stomach Smooth Muscle	stomach
7	chr3:50161800-50165800	Enhancers	Brain Germinal Matrix	brain
8	chr3:50162400-50165200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
9	chr3:50163200-50165600	Enhancers	Duodenum Mucosa	Duodenum
10	chr3:50163600-50165200	Enhancers	Fetal Muscle Leg	muscle
11	chr3:50163600-50165800	Enhancers	Fetal Kidney	kidney
12	chr3:50163600-50166200	Enhancers	Gastric	stomach
13	chr3:50163800-50165200	Enhancers	Osteobl	bone
14	chr3:50164000-50170800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:50164200-50165200	Enhancers	Stomach Mucosa	stomach
16	chr3:50164200-50165600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:50164200-50166000	Enhancers	HepG2	liver
18	chr3:50164200-50170000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:50164400-50169800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:50164400-50174600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:50164600-50172600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:50164600-50174200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:50164800-50165600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:50164800-50167800	Weak transcription	Spleen	Spleen
25	chr3:50164800-50170200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:50165000-50167800	Weak transcription	Fetal Stomach	stomach
27	chr3:50165000-50168000	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:50165000-50170000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:50165000-50170000	Weak transcription	Fetal Brain Male	brain
30	chr3:50165000-50170000	Weak transcription	Fetal Brain Female	brain

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