Variant report

Variant	rs1295641
Chromosome Location	chr1:227070695-227070696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr1:227070131-227070897	GM12878	blood:	n/a	chr1:227070556-227070567 chr1:227070524-227070544
2	MAZ	chr1:227070370-227070982	GM12878	blood:	n/a	n/a
3	STAT3	chr1:227070314-227070770	GM12878	blood:	n/a	chr1:227070556-227070567 chr1:227070524-227070544
4	POLR2A	chr1:227069811-227071003	GM12892	blood:	n/a	n/a
5	FOXM1	chr1:227070350-227070916	GM12878	blood:	n/a	n/a
6	CEBPB	chr1:227070369-227071147	GM12878	blood:	n/a	n/a
7	SMC3	chr1:227070286-227070773	GM12878	blood:	n/a	n/a
8	RELA	chr1:227070068-227071175	GM18951	blood:	n/a	n/a
9	EBF1	chr1:227070043-227071227	GM12878	blood:	n/a	chr1:227070211-227070220
10	SIN3A	chr1:227070429-227070717	GM12878	blood:	n/a	n/a
11	POU2F2	chr1:227070381-227070997	GM12878	blood:	n/a	chr1:227070887-227070900
12	ZNF384	chr1:227070573-227070871	GM12878	blood:	n/a	n/a
13	EP300	chr1:227070457-227070893	GM12878	blood:	n/a	chr1:227070558-227070572 chr1:227070651-227070665
14	RUNX3	chr1:227070281-227070944	GM12878	blood:	n/a	n/a
15	IKZF1	chr1:227070334-227070908	GM12878	blood:	n/a	n/a
16	CUX1	chr1:227070172-227070842	GM12878	blood:	n/a	n/a
17	BCLAF1	chr1:227070402-227070883	GM12878	blood:	n/a	chr1:227070558-227070567
18	POLR2A	chr1:227070354-227070818	GM12891	blood:	n/a	n/a
19	WRNIP1	chr1:227070073-227070873	GM12878	blood:	n/a	n/a
20	RELA	chr1:227070082-227070962	GM19099	blood:	n/a	n/a
21	USF2	chr1:227070094-227070876	GM12878	blood:	n/a	n/a
22	ELK1	chr1:227070288-227070724	GM12878	blood:	n/a	n/a
23	EP300	chr1:227070251-227070856	GM12878	blood:	n/a	chr1:227070558-227070572 chr1:227070651-227070665
24	RFX5	chr1:227070440-227070771	GM12878	blood:	n/a	n/a
25	RUNX3	chr1:227070338-227070987	GM12878	blood:	n/a	n/a
26	ZNF143	chr1:227070432-227070861	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:227070288-227070719	GM12892	blood:	n/a	n/a
28	MTA3	chr1:227069790-227071211	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:227069918-227070907	GM12878	blood:	n/a	n/a
30	TBL1XR1	chr1:227070083-227071108	GM12878	blood:	n/a	n/a
31	NFIC	chr1:227070270-227070894	GM12878	blood:	n/a	n/a
32	ATF2	chr1:227070159-227070797	GM12878	blood:	n/a	n/a
33	PML	chr1:227070385-227071035	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:227070304-227070863	GM12878	blood:	n/a	n/a
35	BHLHE40	chr1:227070119-227070914	GM12878	blood:	n/a	n/a
36	CHD2	chr1:227069840-227070874	GM12878	blood:	n/a	n/a
37	RCOR1	chr1:227070193-227071402	IMR90	lung:	n/a	n/a
38	POLR2A	chr1:227070690-227070780	GM12878	blood:	n/a	n/a
39	MAX	chr1:227070315-227071103	GM12878	blood:	n/a	n/a
40	MXI1	chr1:227070386-227071126	GM12878	blood:	n/a	n/a
41	TBP	chr1:227070096-227070834	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:227070181-227070966	GM12892	blood:	n/a	n/a
43	POLR2A	chr1:227070668-227071340	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227068805..227071011-chr1:227076122..227078773,2	K562	blood:
2	chr1:227058393..227060106-chr1:227070481..227073137,2	MCF-7	breast:

Variant related genes	Relation type
PSEN2	TF binding region
ENSG00000143801	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1046240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150897	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1150900	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11802358	0.88[ASN][1000 genomes]
rs12086302	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12758915	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1289395	0.83[EUR][1000 genomes]
rs1289396	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1295638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1295643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1295647	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1296171	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1794038	0.93[EUR][1000 genomes]
rs1800674	0.87[EUR][1000 genomes]
rs2073489	0.98[ASN][1000 genomes]
rs2236914	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2236915	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2246221	0.90[EUR][1000 genomes]
rs2793461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802268	0.89[ASN][1000 genomes]
rs2855559	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2855560	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2855562	0.87[EUR][1000 genomes]
rs2855564	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4653470	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426541	0.83[ASN][1000 genomes]
rs6426547	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6426548	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6674701	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6688068	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6692729	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6697001	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6697431	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514364	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7518926	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7530245	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7530370	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7547071	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8383	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	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
3	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1295641	PSEN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059800-227075600	Weak transcription	Brain Substantia Nigra	brain
2	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:227060400-227073800	Weak transcription	HepG2	liver
4	chr1:227060400-227077600	Weak transcription	Brain Germinal Matrix	brain
5	chr1:227060600-227077400	Weak transcription	Fetal Brain Female	brain
6	chr1:227062200-227077400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:227062400-227073000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:227062400-227073000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
10	chr1:227063800-227078000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:227064000-227072600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:227064600-227073000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:227065400-227070800	Weak transcription	Brain Anterior Caudate	brain
14	chr1:227065800-227077400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:227066200-227072200	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr1:227066800-227070800	Strong transcription	Aorta	Aorta
17	chr1:227066800-227071400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:227067000-227070800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:227067000-227071800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:227067000-227072000	Strong transcription	Brain Inferior Temporal Lobe	brain
21	chr1:227067000-227081400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:227067200-227072000	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr1:227067600-227071800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:227067800-227075400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:227068200-227073400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:227068400-227071000	Strong transcription	Brain Cingulate Gyrus	brain
27	chr1:227068400-227071200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:227068600-227074200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:227068800-227072800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:227069000-227071200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:227069000-227071200	Weak transcription	Right Ventricle	heart
32	chr1:227069400-227074400	Enhancers	Fetal Thymus	thymus
33	chr1:227069400-227076000	Weak transcription	Brain Angular Gyrus	brain
34	chr1:227069400-227085000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:227069400-227087800	Weak transcription	HMEC	breast
36	chr1:227069400-227102800	Weak transcription	K562	blood
37	chr1:227069600-227070800	Genic enhancers	Placenta	Placenta
38	chr1:227069600-227071800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:227069600-227075000	Genic enhancers	Fetal Muscle Trunk	muscle
40	chr1:227069800-227071000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr1:227069800-227071200	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr1:227069800-227071400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:227069800-227071400	Flanking Active TSS	GM12878-XiMat	blood
44	chr1:227069800-227071600	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr1:227069800-227072200	Enhancers	Stomach Mucosa	stomach
46	chr1:227069800-227074600	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:227069800-227075000	Enhancers	Primary hematopoietic stem cells	blood
48	chr1:227069800-227075000	Genic enhancers	Fetal Muscle Leg	muscle
49	chr1:227070000-227070800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:227070000-227071000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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