Variant report

Variant	rs16846644
Chromosome Location	chr1:227087243-227087244
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227071996..227075968-chr1:227085768..227088327,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSEN2-1	chr1:227087106-227087256	NONHSAT009908

Variant related genes	Relation type
ENSG00000143801	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10799367	0.84[EUR][1000 genomes]
rs10916057	0.87[EUR][1000 genomes]
rs10916059	0.96[EUR][1000 genomes]
rs11580744	0.90[EUR][1000 genomes]
rs11588886	0.97[EUR][1000 genomes]
rs12119853	0.85[EUR][1000 genomes]
rs12123818	0.97[EUR][1000 genomes]
rs12125811	0.87[EUR][1000 genomes]
rs12127440	0.87[EUR][1000 genomes]
rs12130732	0.97[EUR][1000 genomes]
rs12138310	0.82[EUR][1000 genomes]
rs12143886	0.86[EUR][1000 genomes]
rs12403248	0.87[EUR][1000 genomes]
rs12405779	0.87[EUR][1000 genomes]
rs12733650	0.89[EUR][1000 genomes]
rs12747261	0.98[EUR][1000 genomes]
rs12760155	0.96[EUR][1000 genomes]
rs1794035	0.81[CEU][hapmap]
rs1800672	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800673	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800681	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2236912	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3213436	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs34081886	0.96[EUR][1000 genomes]
rs35029375	0.95[EUR][1000 genomes]
rs35213802	0.97[EUR][1000 genomes]
rs35396772	0.89[EUR][1000 genomes]
rs35519961	0.97[EUR][1000 genomes]
rs35744376	0.83[EUR][1000 genomes]
rs3820649	0.97[EUR][1000 genomes]
rs3829979	0.97[EUR][1000 genomes]
rs6426554	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs6676065	0.97[EUR][1000 genomes]
rs6676067	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6680780	0.96[EUR][1000 genomes]
rs71648404	0.97[EUR][1000 genomes]
rs732479	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7512804	0.90[EUR][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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16846644	PSEN2	cis	cerebellum	SCAN
rs16846644	PSEN2	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:227069400-227087800	Weak transcription	HMEC	breast
3	chr1:227069400-227102800	Weak transcription	K562	blood
4	chr1:227070800-227088200	Weak transcription	Fetal Brain Male	brain
5	chr1:227071000-227089000	Strong transcription	Stomach Smooth Muscle	stomach
6	chr1:227071200-227088400	Weak transcription	Hela-S3	cervix
7	chr1:227071200-227091400	Weak transcription	Osteobl	bone
8	chr1:227071800-227102400	Weak transcription	Small Intestine	intestine
9	chr1:227072200-227091800	Weak transcription	Fetal Kidney	kidney
10	chr1:227072200-227100400	Weak transcription	Stomach Mucosa	stomach
11	chr1:227073400-227088600	Strong transcription	Fetal Stomach	stomach
12	chr1:227073400-227092200	Strong transcription	Pancreas	Pancrea
13	chr1:227073800-227100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:227074200-227091800	Weak transcription	Fetal Heart	heart
15	chr1:227074800-227090000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:227074800-227090200	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:227075000-227087400	Weak transcription	Primary B cells from cord blood	blood
18	chr1:227075000-227088800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:227075200-227091800	Weak transcription	Right Atrium	heart
20	chr1:227075400-227088800	Strong transcription	Liver	Liver
21	chr1:227075600-227088200	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr1:227076600-227087400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:227078600-227091600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:227079800-227097200	Weak transcription	Brain Germinal Matrix	brain
25	chr1:227080000-227094800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:227080200-227090600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:227080400-227087400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:227080400-227088200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:227080400-227090000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:227080600-227087400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:227080600-227088400	Strong transcription	Left Ventricle	heart
32	chr1:227080600-227088800	Strong transcription	Adipose Nuclei	Adipose
33	chr1:227080600-227089000	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:227080600-227089800	Strong transcription	Fetal Muscle Trunk	muscle
35	chr1:227080800-227093600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:227081000-227088800	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:227081800-227089200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:227082400-227091000	Weak transcription	NHLF	lung
39	chr1:227082600-227089000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:227082800-227089000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:227082800-227110600	Weak transcription	Fetal Brain Female	brain
42	chr1:227083000-227089800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:227083000-227092000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:227083200-227087400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:227083200-227087400	Weak transcription	A549	lung
46	chr1:227083200-227091400	Weak transcription	Colonic Mucosa	Colon
47	chr1:227083200-227099400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:227083200-227126600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:227083400-227087800	Weak transcription	Esophagus	oesophagus
50	chr1:227083400-227090200	Weak transcription	NHEK	skin

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