Variant report

Variant	rs2003485
Chromosome Location	chr3:50176589-50176590
allele	A/G
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	chr3:50175980..50179731-chr3:50201223..50204362,3	K562	blood:
3	chr3:50172563..50177055-chr3:50182695..50185570,4	MCF-7	breast:
4	chr3:50170263..50171999-chr3:50174884..50177139,2	MCF-7	breast:
5	chr3:50176235..50178940-chr3:50182540..50184330,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000001617	Chromatin interaction
ENSG00000235016	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11916999	0.87[ASN][1000 genomes]
rs11920034	0.87[ASN][1000 genomes]
rs11924670	0.87[ASN][1000 genomes]
rs11924711	0.87[ASN][1000 genomes]
rs11928995	0.87[ASN][1000 genomes]
rs12486470	0.87[ASN][1000 genomes]
rs12492291	0.87[ASN][1000 genomes]
rs12494077	0.87[ASN][1000 genomes]
rs12494172	0.87[ASN][1000 genomes]
rs12494916	0.87[ASN][1000 genomes]
rs12495114	0.87[ASN][1000 genomes]
rs12631248	0.87[ASN][1000 genomes]
rs12632751	0.87[ASN][1000 genomes]
rs12636045	0.87[ASN][1000 genomes]
rs12636232	0.87[ASN][1000 genomes]
rs13100903	0.94[ASN][1000 genomes]
rs2023951	0.87[ASN][1000 genomes]
rs2023952	0.87[ASN][1000 genomes]
rs35333166	0.87[ASN][1000 genomes]
rs59802870	0.87[ASN][1000 genomes]
rs62260770	0.87[ASN][1000 genomes]
rs62260771	0.87[ASN][1000 genomes]
rs62263584	0.87[ASN][1000 genomes]
rs62263586	0.87[ASN][1000 genomes]
rs62263588	0.87[ASN][1000 genomes]
rs62263590	0.87[ASN][1000 genomes]
rs62263591	0.87[ASN][1000 genomes]
rs62263596	0.87[ASN][1000 genomes]
rs62263600	0.87[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2003485	RBM6	cis	Whole Blood	GTEx
rs2003485	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2003485	RBM6	cis	Artery Tibial	GTEx
rs2003485	RBM6	cis	Nerve Tibial	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50171200-50178400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:50172400-50176600	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr3:50173200-50178000	Enhancers	Fetal Lung	lung
4	chr3:50173400-50176600	Enhancers	Fetal Stomach	stomach
5	chr3:50173400-50178200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr3:50173600-50176800	Enhancers	Fetal Muscle Leg	muscle
7	chr3:50173600-50177400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:50173600-50177400	Enhancers	Fetal Kidney	kidney
9	chr3:50173800-50177400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:50173800-50177800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:50174000-50177200	Enhancers	Placenta	Placenta
12	chr3:50174200-50178000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:50174400-50177000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:50174400-50178200	Enhancers	Esophagus	oesophagus
15	chr3:50174800-50177600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr3:50174800-50178000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:50175000-50177000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:50175000-50177400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:50175000-50177800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:50175200-50177600	Enhancers	Fetal Thymus	thymus
21	chr3:50175200-50178600	Enhancers	Spleen	Spleen
22	chr3:50175400-50177200	Enhancers	NHLF	lung
23	chr3:50175400-50177400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr3:50175400-50177600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:50175400-50177600	Bivalent Enhancer	Fetal Intestine Small	intestine
26	chr3:50175400-50177600	Enhancers	Lung	lung
27	chr3:50175400-50178000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr3:50175600-50176600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:50175600-50176600	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr3:50175600-50176600	Enhancers	Adipose Nuclei	Adipose
31	chr3:50175600-50176800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr3:50175600-50176800	Enhancers	Dnd41	blood
33	chr3:50175600-50176800	Enhancers	Hela-S3	cervix
34	chr3:50175600-50176800	Enhancers	NH-A	brain
35	chr3:50175600-50177000	Enhancers	HMEC	breast
36	chr3:50175600-50177200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:50175600-50177600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr3:50175600-50177600	Enhancers	Fetal Brain Male	brain
39	chr3:50175800-50176600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:50175800-50176600	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr3:50175800-50176600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr3:50175800-50176600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:50175800-50176600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:50175800-50176600	Enhancers	Stomach Mucosa	stomach
45	chr3:50175800-50176800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr3:50175800-50177200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:50175800-50177400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:50175800-50177600	Enhancers	Primary hematopoietic stem cells	blood
49	chr3:50176000-50176600	Active TSS	H9 Cell Line	embryonic stem cell
50	chr3:50176000-50176600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links