Variant report

Variant	rs2014004
Chromosome Location	chr3:50175940-50175941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50175604..50177839-chr3:50192522..50194545,2	K562	blood:
2	chr3:50172563..50177055-chr3:50182695..50185570,4	MCF-7	breast:
3	chr3:50170263..50171999-chr3:50174884..50177139,2	MCF-7	breast:
4	chr3:50171431..50173846-chr3:50174182..50176296,2	K562	blood:

Variant related genes	Relation type
ENSG00000001617	Chromatin interaction
ENSG00000235016	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1046956	1.00[ASN][1000 genomes]
rs1061474	0.88[YRI][hapmap]
rs1138536	0.88[YRI][hapmap]
rs13059311	1.00[ASN][1000 genomes]
rs13064381	1.00[ASN][1000 genomes]
rs13067082	1.00[ASN][1000 genomes]
rs13071931	0.88[YRI][hapmap]
rs13091525	1.00[ASN][1000 genomes]
rs13095697	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097720	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs14321	1.00[ASN][1000 genomes]
rs17225749	1.00[ASN][1000 genomes]
rs17304079	0.88[YRI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657664	0.82[YRI][hapmap]
rs2189691	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2526384	1.00[ASN][1000 genomes]
rs2526387	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526397	1.00[ASN][1000 genomes]
rs2526398	1.00[ASN][1000 genomes]
rs2526747	0.88[YRI][hapmap]
rs2624826	0.88[YRI][hapmap]
rs2624833	1.00[ASN][1000 genomes]
rs2624841	1.00[ASN][1000 genomes]
rs2624846	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35012435	1.00[ASN][1000 genomes]
rs35375092	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35491931	1.00[ASN][1000 genomes]
rs35849525	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774734	0.88[YRI][hapmap]
rs55924524	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260755	1.00[ASN][1000 genomes]
rs62262061	1.00[ASN][1000 genomes]
rs62262106	1.00[ASN][1000 genomes]
rs62262118	1.00[ASN][1000 genomes]
rs62263602	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762477	0.88[YRI][hapmap]
rs6785500	0.93[YRI][hapmap]
rs6787892	1.00[ASN][1000 genomes]
rs7061	0.88[YRI][hapmap]
rs71326904	1.00[ASN][1000 genomes]
rs71326915	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615318	0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs7635601	0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs7648652	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858297	1.00[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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2014004	RBM6	cis	Whole Blood	GTEx
rs2014004	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2014004	RBM6	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50151000-50176400	Weak transcription	Right Atrium	heart
2	chr3:50171200-50178400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:50172400-50176600	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr3:50173200-50178000	Enhancers	Fetal Lung	lung
5	chr3:50173400-50176600	Enhancers	Fetal Stomach	stomach
6	chr3:50173400-50178200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr3:50173600-50176800	Enhancers	Fetal Muscle Leg	muscle
8	chr3:50173600-50177400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:50173600-50177400	Enhancers	Fetal Kidney	kidney
10	chr3:50173800-50177400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:50173800-50177800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:50174000-50176400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:50174000-50177200	Enhancers	Placenta	Placenta
14	chr3:50174200-50176000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr3:50174200-50178000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:50174400-50176000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:50174400-50176000	Enhancers	NHEK	skin
18	chr3:50174400-50177000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:50174400-50178200	Enhancers	Esophagus	oesophagus
20	chr3:50174600-50176000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:50174600-50176000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:50174600-50176000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:50174600-50176200	Weak transcription	Right Ventricle	heart
24	chr3:50174800-50177600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr3:50174800-50178000	Enhancers	H1 Cell Line	embryonic stem cell
26	chr3:50175000-50176000	Weak transcription	Brain Anterior Caudate	brain
27	chr3:50175000-50176000	Enhancers	Fetal Brain Female	brain
28	chr3:50175000-50177000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:50175000-50177400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr3:50175000-50177800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:50175200-50176000	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr3:50175200-50176000	Enhancers	Brain Germinal Matrix	brain
33	chr3:50175200-50176000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:50175200-50176200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:50175200-50177600	Enhancers	Fetal Thymus	thymus
36	chr3:50175200-50178600	Enhancers	Spleen	Spleen
37	chr3:50175400-50176000	Enhancers	H9 Cell Line	embryonic stem cell
38	chr3:50175400-50176000	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr3:50175400-50176000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:50175400-50176000	Enhancers	HUVEC	blood vessel
41	chr3:50175400-50176200	Enhancers	Stomach Smooth Muscle	stomach
42	chr3:50175400-50177200	Enhancers	NHLF	lung
43	chr3:50175400-50177400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr3:50175400-50177600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:50175400-50177600	Bivalent Enhancer	Fetal Intestine Small	intestine
46	chr3:50175400-50177600	Enhancers	Lung	lung
47	chr3:50175400-50178000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr3:50175600-50176000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:50175600-50176000	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr3:50175600-50176400	Enhancers	Muscle Satellite Cultured Cells	--

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