Variant report

Variant	rs2292491
Chromosome Location	chr12:39760747-39760748
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39759047..39762172-chr12:39834495..39838400,6	MCF-7	breast:
2	chr12:39757176..39762110-chr12:39835391..39838507,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252974	Chromatin interaction
ENSG00000139116	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11172144	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs11172162	0.93[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs12227286	1.00[JPT][hapmap]
rs12228013	0.93[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1512941	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512943	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17126997	1.00[ASW][hapmap];0.86[CEU][hapmap];0.81[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17127029	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127094	0.92[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127100	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs17127138	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2137495	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271478	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4294600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs4620763	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56858582	0.84[AFR][1000 genomes]
rs57196300	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58891998	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59967849	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61039034	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7135918	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307730	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7308138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73086885	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088816	0.83[ASN][1000 genomes]
rs7309234	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs7312611	0.90[JPT][hapmap]
rs7956823	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7966841	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];1.00[ASN][1000 genomes]
rs7970819	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970944	0.83[ASN][1000 genomes]
rs7976275	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978854	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963637	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv558589	chr12:39667861-39768356	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2292491	ABCD2	cis	multi-tissue	Pritchard
rs2292491	LRRK2	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39696600-39762200	Weak transcription	Fetal Brain Male	brain
2	chr12:39697800-39771800	Weak transcription	Fetal Kidney	kidney
3	chr12:39721000-39770600	Weak transcription	Gastric	stomach
4	chr12:39722800-39767200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:39726400-39766600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:39726600-39766600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr12:39726600-39766600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:39726600-39766800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:39726800-39762200	Weak transcription	Placenta	Placenta
10	chr12:39726800-39766600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:39727000-39761400	Weak transcription	Fetal Intestine Small	intestine
12	chr12:39727000-39762400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:39727000-39767000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:39727000-39779200	Weak transcription	Aorta	Aorta
15	chr12:39735200-39761400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:39735600-39766600	Weak transcription	HMEC	breast
17	chr12:39735600-39766600	Weak transcription	NHEK	skin
18	chr12:39737400-39766600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:39740600-39761200	Weak transcription	Brain Substantia Nigra	brain
20	chr12:39742600-39761400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr12:39743000-39766800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:39743200-39765800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr12:39745000-39762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:39745000-39778600	Weak transcription	Pancreas	Pancrea
25	chr12:39748200-39764000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:39748400-39765800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr12:39748800-39764000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:39749000-39764200	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:39749800-39761200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:39750200-39761600	Weak transcription	Small Intestine	intestine
31	chr12:39750200-39765400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:39750400-39762000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:39750800-39762200	Weak transcription	HepG2	liver
34	chr12:39751200-39761200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:39751200-39762400	Weak transcription	Adipose Nuclei	Adipose
36	chr12:39751200-39762600	Weak transcription	K562	blood
37	chr12:39751400-39770400	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:39751600-39771800	Weak transcription	Brain Anterior Caudate	brain
39	chr12:39752000-39765400	Weak transcription	Left Ventricle	heart
40	chr12:39752200-39762200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:39752200-39762600	Weak transcription	Fetal Brain Female	brain
42	chr12:39752200-39765400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:39752200-39766400	Weak transcription	Fetal Heart	heart
44	chr12:39752200-39767600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr12:39752200-39769000	Weak transcription	Ovary	ovary
46	chr12:39752200-39769200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:39756000-39762400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:39756200-39766600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:39756200-39767600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr12:39757000-39764000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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