Variant report

Variant	rs7652530
Chromosome Location	chr3:140956248-140956249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:140948502..140951500-chr3:140954182..140956854,2	MCF-7	breast:
2	chr3:140954329..140957093-chr3:140957221..140960303,3	K562	blood:

Variant related genes	Relation type
ENSG00000155893	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1026716	0.85[TSI][hapmap]
rs10935425	0.82[MEX][hapmap];0.80[TSI][hapmap]
rs10935427	0.83[MEX][hapmap];0.86[TSI][hapmap]
rs12486843	0.81[EUR][1000 genomes]
rs13065438	0.81[EUR][1000 genomes]
rs13069904	0.96[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs1511371	0.91[EUR][1000 genomes]
rs1511372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1511373	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1877222	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1877223	0.87[MEX][hapmap]
rs2048459	0.93[EUR][1000 genomes]
rs2137016	0.83[MEX][hapmap]
rs2291039	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683585	0.93[EUR][1000 genomes]
rs4683586	0.96[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs6439988	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6779870	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7613113	0.90[EUR][1000 genomes]
rs967526	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs9875630	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7652530	ACPL2	cis	parietal	SCAN
rs7652530	XRN1	cis	parietal	SCAN
rs7652530	ACPL2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140951600-140956400	Weak transcription	Psoas Muscle	Psoas
2	chr3:140951600-140956600	Weak transcription	Gastric	stomach
3	chr3:140951600-140957000	Weak transcription	Aorta	Aorta
4	chr3:140951600-140959000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:140951600-140979000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:140951800-140956400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:140951800-140956400	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:140951800-140956600	Weak transcription	Fetal Lung	lung
9	chr3:140951800-140956800	Weak transcription	Right Atrium	heart
10	chr3:140951800-140956800	Weak transcription	Stomach Mucosa	stomach
11	chr3:140951800-140958800	Weak transcription	Osteobl	bone
12	chr3:140951800-140959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:140951800-140960200	Weak transcription	Esophagus	oesophagus
14	chr3:140951800-140960400	Weak transcription	Brain Substantia Nigra	brain
15	chr3:140951800-140962000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:140951800-140962200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:140952000-140956600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:140952000-140956600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:140952000-140956600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:140952000-140956800	Weak transcription	HSMM	muscle
21	chr3:140952000-140957000	Weak transcription	Brain Anterior Caudate	brain
22	chr3:140952000-140958400	Weak transcription	Fetal Kidney	kidney
23	chr3:140952000-140959000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:140952000-140959000	Weak transcription	Placenta	Placenta
25	chr3:140952000-140959600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:140952000-140962000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr3:140952200-140958000	Weak transcription	Right Ventricle	heart
28	chr3:140952400-140959600	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:140952600-140956400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:140952600-140957800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:140953000-140956800	Enhancers	Fetal Heart	heart
32	chr3:140953000-140958800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:140953200-140956400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr3:140953200-140959200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:140953400-140958800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:140953600-140956400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:140953600-140959600	Genic enhancers	Fetal Thymus	thymus
38	chr3:140953600-140960200	Weak transcription	Spleen	Spleen
39	chr3:140953800-140956400	Weak transcription	Fetal Brain Female	brain
40	chr3:140953800-140956600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:140953800-140958400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:140954000-140959200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:140954200-140959200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:140954400-140956800	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:140954800-140957000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:140954800-140957200	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr3:140954800-140957200	Enhancers	Primary hematopoietic stem cells	blood
48	chr3:140954800-140958600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:140955000-140956400	Enhancers	Primary T cells from cord blood	blood
50	chr3:140955000-140956600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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