Variant report

Variant	rs2008877
Chromosome Location	chr3:50162291-50162292
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50160874..50163640-chr3:50208443..50212191,3	MCF-7	breast:
2	chr3:50159863..50162699-chr3:50227102..50229015,2	MCF-7	breast:
3	chr3:50157890..50164898-chr3:50186493..50191745,15	MCF-7	breast:
4	chr3:50126440..50128004-chr3:50161064..50162835,2	MCF-7	breast:
5	chr3:50160998..50164207-chr3:50182321..50186383,5	MCF-7	breast:
6	chr3:50160721..50162724-chr3:50168795..50173383,5	K562	blood:
7	chr3:50161160..50162683-chr3:50271555..50274143,2	MCF-7	breast:
8	chr3:50159660..50164036-chr3:50192840..50194687,5	MCF-7	breast:
9	chr3:50159102..50161217-chr3:50161241..50163893,2	MCF-7	breast:
10	chr3:50159456..50162319-chr3:50219571..50221770,3	K562	blood:
11	chr3:50160797..50162684-chr3:50168795..50170458,2	K562	blood:
12	chr3:50157840..50167526-chr3:50182100..50196634,43	MCF-7	breast:
13	chr3:50161300..50163134-chr3:50195216..50197721,2	MCF-7	breast:
14	chr3:50160236..50162661-chr3:50199284..50201968,2	MCF-7	breast:
15	chr3:50161158..50162921-chr3:50305977..50308672,2	MCF-7	breast:
16	chr3:50160600..50163125-chr3:50165110..50166972,2	K562	blood:
17	chr3:50162229..50165038-chr3:50305683..50307880,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000001617	Chromatin interaction
ENSG00000114353	Chromatin interaction
ENSG00000235016	Chromatin interaction
ENSG00000003756	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000207922	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10049087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11130228	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11130233	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs12496973	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs13060128	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs2013208	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2071206	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2071207	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2240326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2240327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2240329	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2245365	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs2252833	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs2301166	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2353579	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2526743	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526748	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes]
rs2526751	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs2526754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2624816	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2624823	0.90[EUR][1000 genomes]
rs2624824	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2624825	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2624843	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs2624847	0.82[GIH][hapmap];0.92[JPT][hapmap]
rs2624853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2856234	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2856236	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2883057	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs34831713	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3733133	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3774733	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4688686	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4688689	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs4688690	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs4688755	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs4688758	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs6446193	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs6765484	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs6771546	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs6772095	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs6792892	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs7428430	0.91[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs7613875	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs7621026	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs7621352	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs7628058	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs7642934	0.95[EUR][1000 genomes]
rs9311446	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes]
rs9814664	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs9856572	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9861216	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap]
rs9866695	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 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
17	esv3346703	chr3:50161798-50164121	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2008877	RBM6	cis	lung	GTEx
rs2008877	RBM6	cis	Esophagus Muscularis	GTEx
rs2008877	RBM6	cis	Thyroid	GTEx
rs2008877	RBM6	cis	Adipose Subcutaneous	GTEx
rs2008877	RBM6	cis	Whole Blood	GTEx
rs2008877	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs2008877	RBM6	cis	Heart Left Ventricle	GTEx
rs2008877	RBM6	cis	Nerve Tibial	GTEx
rs2008877	RBM6	cis	Stomach	GTEx
rs2008877	RBM6	cis	Artery Aorta	GTEx
rs2008877	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2008877	RBM6	cis	Esophagus Mucosa	GTEx
rs2008877	RBM6	cis	Artery Tibial	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50143200-50163200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:50151000-50176400	Weak transcription	Right Atrium	heart
3	chr3:50156400-50163800	Weak transcription	K562	blood
4	chr3:50157800-50163200	Weak transcription	Brain Substantia Nigra	brain
5	chr3:50157800-50164400	Weak transcription	Small Intestine	intestine
6	chr3:50158600-50163200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:50158600-50163200	Weak transcription	Left Ventricle	heart
8	chr3:50158600-50164200	Weak transcription	Aorta	Aorta
9	chr3:50158600-50164400	Weak transcription	HSMMtube	muscle
10	chr3:50158800-50162400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:50158800-50162600	Weak transcription	Primary B cells from cord blood	blood
12	chr3:50159200-50162400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:50159200-50162600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:50159200-50163200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:50159200-50163800	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr3:50159200-50165000	Enhancers	Placenta	Placenta
17	chr3:50159200-50165200	Enhancers	Fetal Lung	lung
18	chr3:50159400-50162400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:50159400-50162600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:50159400-50162800	Weak transcription	Fetal Brain Male	brain
21	chr3:50159400-50163400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:50159600-50163200	Enhancers	Fetal Muscle Leg	muscle
23	chr3:50159600-50163400	Weak transcription	HepG2	liver
24	chr3:50159600-50164800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:50159800-50162400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:50159800-50164200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:50159800-50168600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:50160000-50162800	Enhancers	Esophagus	oesophagus
29	chr3:50160000-50163600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:50160200-50163200	Weak transcription	Fetal Brain Female	brain
31	chr3:50160400-50162400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:50160600-50162400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:50160600-50163000	Weak transcription	Colonic Mucosa	Colon
34	chr3:50160600-50164400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:50160600-50165000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:50160800-50162600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:50160800-50164600	Enhancers	H1 Cell Line	embryonic stem cell
38	chr3:50160800-50164600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:50160800-50165000	Enhancers	Hela-S3	cervix
40	chr3:50161000-50162400	Enhancers	Fetal Intestine Large	intestine
41	chr3:50161000-50162600	Enhancers	NHEK	skin
42	chr3:50161000-50164400	Enhancers	Placenta Amnion	Placenta Amnion
43	chr3:50161000-50164800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:50161200-50162400	Enhancers	Primary T cells fromperipheralblood	blood
45	chr3:50161200-50162400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:50161200-50162800	Weak transcription	Primary T cells from cord blood	blood
47	chr3:50161200-50163600	Weak transcription	Right Ventricle	heart
48	chr3:50161200-50164000	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr3:50161200-50164200	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr3:50161200-50164600	Enhancers	HUES6 Cell Line	embryonic stem cell

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