Variant report

Variant	rs2570230
Chromosome Location	chr15:52109978-52109979
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52107930..52111784-chr15:52120975..52124662,5	MCF-7	breast:
2	chr15:52108842..52110783-chr15:52116396..52117937,2	MCF-7	breast:
3	chr15:52089329..52092071-chr15:52108088..52110534,3	MCF-7	breast:
4	chr15:52109002..52111663-chr15:52121373..52123831,2	K562	blood:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1133878	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964482	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16964483	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17611465	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1863429	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1972419	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991267	1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs2016057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124587	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2258248	1.00[CHB][hapmap]
rs2448810	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2554354	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554355	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554358	0.96[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570243	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593169	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2593181	1.00[CHB][hapmap]
rs2593184	0.83[AMR][1000 genomes]
rs2606128	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2606130	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606133	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606147	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622765	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2623245	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623247	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623251	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623263	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623270	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652597	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28522862	1.00[ASN][1000 genomes]
rs28654101	1.00[ASN][1000 genomes]
rs28876142	1.00[ASN][1000 genomes]
rs2959296	1.00[CHB][hapmap]
rs55922236	1.00[ASN][1000 genomes]
rs691738	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71472920	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2570230	RP11-707P17.1	cis	Nerve Tibial	GTEx
rs2570230	SCG3	cis	Brain Pons	GTEx
rs2570230	SCG3	cis	Temporal Cortex	GTEx
rs2570230	SCG3	cis	Cerebellum	GTEx
rs2570230	SCG3	cis	Frontal Cortex	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52061600-52112000	Weak transcription	NHLF	lung
2	chr15:52099800-52110000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr15:52099800-52110400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:52099800-52110400	Weak transcription	Left Ventricle	heart
5	chr15:52099800-52113800	Weak transcription	Aorta	Aorta
6	chr15:52100000-52110200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:52100000-52113200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:52101200-52110200	Weak transcription	NHDF-Ad	bronchial
9	chr15:52101600-52113000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:52101800-52110200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:52102000-52113400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:52103000-52111600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr15:52104400-52113400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr15:52104400-52113600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:52105600-52113200	Weak transcription	Primary B cells from cord blood	blood
16	chr15:52105800-52111600	Weak transcription	Thymus	Thymus
17	chr15:52106600-52111800	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:52106800-52110200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:52106800-52113400	Weak transcription	Brain Germinal Matrix	brain
20	chr15:52107000-52110600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr15:52107000-52113200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:52107000-52113600	Weak transcription	Primary T cells from cord blood	blood
23	chr15:52107000-52113800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:52107200-52112800	Weak transcription	Brain Angular Gyrus	brain
25	chr15:52107200-52113000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr15:52107200-52121400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:52108000-52110000	Enhancers	Fetal Intestine Small	intestine
28	chr15:52108200-52110000	Enhancers	Fetal Intestine Large	intestine
29	chr15:52108800-52110200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:52109000-52110000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr15:52109400-52110000	Enhancers	Esophagus	oesophagus
32	chr15:52109400-52110000	Enhancers	Lung	lung
33	chr15:52109400-52110000	Enhancers	Spleen	Spleen
34	chr15:52109400-52110200	Enhancers	Gastric	stomach
35	chr15:52109400-52110400	Strong transcription	Fetal Brain Female	brain
36	chr15:52109400-52110600	Strong transcription	Fetal Stomach	stomach
37	chr15:52109800-52111400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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