Variant report

Variant	rs6439985
Chromosome Location	chr3:140956014-140956015
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: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11715472	1.00[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs1397798	0.82[EUR][1000 genomes]
rs1511370	0.82[EUR][1000 genomes]
rs1511376	0.80[CEU][hapmap]
rs1511378	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs1511386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1877219	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1993904	0.87[GIH][hapmap]
rs2063464	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2169868	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4308250	1.00[JPT][hapmap]
rs4683584	0.82[EUR][1000 genomes]
rs4683588	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs4683592	1.00[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs6439984	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6439990	0.94[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6439993	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs6798093	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6803826	1.00[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs7629077	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7643346	0.87[GIH][hapmap]
rs899349	0.82[EUR][1000 genomes]
rs9289627	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs9817668	0.82[EUR][1000 genomes]
rs9880195	1.00[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs9990218	0.86[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6439985	ACPL2	cis	multi-tissue	Pritchard

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140951600-140956200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:140951600-140956400	Weak transcription	Psoas Muscle	Psoas
3	chr3:140951600-140956600	Weak transcription	Gastric	stomach
4	chr3:140951600-140957000	Weak transcription	Aorta	Aorta
5	chr3:140951600-140959000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:140951600-140979000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:140951800-140956400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:140951800-140956400	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:140951800-140956600	Weak transcription	Fetal Lung	lung
10	chr3:140951800-140956800	Weak transcription	Right Atrium	heart
11	chr3:140951800-140956800	Weak transcription	Stomach Mucosa	stomach
12	chr3:140951800-140958800	Weak transcription	Osteobl	bone
13	chr3:140951800-140959000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:140951800-140960200	Weak transcription	Esophagus	oesophagus
15	chr3:140951800-140960400	Weak transcription	Brain Substantia Nigra	brain
16	chr3:140951800-140962000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:140951800-140962200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:140952000-140956200	Weak transcription	Brain Angular Gyrus	brain
19	chr3:140952000-140956200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:140952000-140956600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:140952000-140956600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:140952000-140956600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:140952000-140956800	Weak transcription	HSMM	muscle
24	chr3:140952000-140957000	Weak transcription	Brain Anterior Caudate	brain
25	chr3:140952000-140958400	Weak transcription	Fetal Kidney	kidney
26	chr3:140952000-140959000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:140952000-140959000	Weak transcription	Placenta	Placenta
28	chr3:140952000-140959600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:140952000-140962000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr3:140952200-140958000	Weak transcription	Right Ventricle	heart
31	chr3:140952400-140959600	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:140952600-140956400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr3:140952600-140957800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:140952800-140956200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:140953000-140956800	Enhancers	Fetal Heart	heart
36	chr3:140953000-140958800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:140953200-140956400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr3:140953200-140959200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:140953400-140958800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:140953600-140956400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:140953600-140959600	Genic enhancers	Fetal Thymus	thymus
42	chr3:140953600-140960200	Weak transcription	Spleen	Spleen
43	chr3:140953800-140956400	Weak transcription	Fetal Brain Female	brain
44	chr3:140953800-140956600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:140953800-140958400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:140954000-140959200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:140954200-140956200	Weak transcription	Fetal Brain Male	brain
48	chr3:140954200-140959200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:140954400-140956800	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr3:140954600-140956200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links