Variant report

Variant	rs6439989
Chromosome Location	chr3:140960421-140960422
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:140960420..140963104-chr3:140988791..140990296,2	K562	blood:
2	chr3:140949314..140952650-chr3:140959989..140963598,3	MCF-7	breast:
3	chr3:140960166..140963166-chr3:140967948..140970939,3	MCF-7	breast:
4	chr3:140958319..140960970-chr3:140982966..140985127,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155893	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11710222	0.95[EUR][1000 genomes]
rs11713226	0.89[CEU][hapmap];0.90[CHB][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs11713257	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs16851191	1.00[CEU][hapmap];0.89[YRI][hapmap];0.96[EUR][1000 genomes]
rs2292401	0.83[EUR][1000 genomes]
rs2292402	0.84[EUR][1000 genomes]
rs4683587	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[EUR][1000 genomes]
rs55923220	0.94[EUR][1000 genomes]
rs56163421	0.95[EUR][1000 genomes]
rs56254804	0.94[EUR][1000 genomes]
rs6439986	0.84[EUR][1000 genomes]
rs6439987	0.84[EUR][1000 genomes]
rs6762331	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[EUR][1000 genomes]
rs73869537	0.95[EUR][1000 genomes]
rs7618821	0.94[CEU][hapmap];0.90[CHB][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs7629005	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[EUR][1000 genomes]
rs7636976	0.84[EUR][1000 genomes]
rs9682606	0.81[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.85[YRI][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6439989	ACPL2	cis	Liver	GTEx
rs6439989	RBP2	cis	parietal	SCAN
rs6439989	HSS00305011	cis	multi-tissue	Pritchard
rs6439989	ACPL2	cis	parietal	SCAN
rs6439989	ACPL2	cis	cerebellum	SCAN
rs6439989	TRPC1	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140951600-140979000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:140951800-140962000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:140951800-140962200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:140952000-140962000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr3:140955000-140960600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:140955000-140961800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:140955200-140962000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr3:140955200-140980600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:140955400-140968400	Genic enhancers	Dnd41	blood
10	chr3:140955400-140985800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:140956200-140962600	Enhancers	Fetal Brain Male	brain
12	chr3:140956400-140962600	Genic enhancers	Thymus	Thymus
13	chr3:140956600-140962600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr3:140956600-140962600	Enhancers	Fetal Muscle Leg	muscle
15	chr3:140956600-140962600	Enhancers	Left Ventricle	heart
16	chr3:140957000-140961800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:140957000-140962200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:140957400-140961800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr3:140957400-140962000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:140957400-140967800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:140957400-140967800	Weak transcription	Gastric	stomach
22	chr3:140957400-141001000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:140957600-140961600	Enhancers	Fetal Brain Female	brain
24	chr3:140957600-140961800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:140957800-140961800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:140957800-140962000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:140957800-140973600	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:140958000-140961200	Enhancers	Right Ventricle	heart
29	chr3:140958000-140962600	Enhancers	Right Atrium	heart
30	chr3:140958200-140961000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr3:140958200-140961200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:140958200-140961200	Enhancers	Brain Angular Gyrus	brain
33	chr3:140958200-140961200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:140958200-140961400	Enhancers	Brain Cingulate Gyrus	brain
35	chr3:140958400-140962000	Enhancers	Brain Anterior Caudate	brain
36	chr3:140958400-140962200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:140958600-140960600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:140958600-140960600	Enhancers	Aorta	Aorta
39	chr3:140958600-140961200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:140958600-140961800	Enhancers	Fetal Stomach	stomach
41	chr3:140958600-140962200	Enhancers	Lung	lung
42	chr3:140958600-140962400	Enhancers	Psoas Muscle	Psoas
43	chr3:140958800-140961000	Enhancers	HMEC	breast
44	chr3:140958800-140961200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:140958800-140962200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:140958800-140962400	Enhancers	Osteobl	bone
47	chr3:140959000-140961200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:140959000-140961400	Enhancers	Placenta	Placenta
49	chr3:140959000-140962200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:140959000-140962200	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links