Variant report

Variant	rs3213436
Chromosome Location	chr1:227081305-227081306
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	chr1:227072686..227075297-chr1:227079508..227082129,3	K562	blood:
2	chr1:227063874..227066086-chr1:227080166..227082122,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10799367	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916057	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10916059	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11580744	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11588886	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12119853	0.88[EUR][1000 genomes]
rs12123818	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125811	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12127440	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12130732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132893	0.93[JPT][hapmap]
rs12138310	0.83[EUR][1000 genomes]
rs12143886	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12403248	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12405779	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12733650	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12747261	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12760155	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16846644	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs1794035	0.81[CEU][hapmap]
rs1800672	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs1800673	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes]
rs1800681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2236912	0.95[EUR][1000 genomes]
rs34081886	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35029375	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35213802	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35244407	0.82[EUR][1000 genomes]
rs35396772	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35519961	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35744376	0.86[EUR][1000 genomes]
rs3820649	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829979	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426554	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676065	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6676067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680780	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71648404	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7512804	0.93[EUR][1000 genomes];0.82[ASN][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
rs3213436	PSEN2	cis	parietal	SCAN
rs3213436	PSEN2	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
3	chr1:227067000-227081400	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:227069400-227085000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:227069400-227087800	Weak transcription	HMEC	breast
6	chr1:227069400-227102800	Weak transcription	K562	blood
7	chr1:227070800-227088200	Weak transcription	Fetal Brain Male	brain
8	chr1:227071000-227089000	Strong transcription	Stomach Smooth Muscle	stomach
9	chr1:227071200-227086800	Weak transcription	NHDF-Ad	bronchial
10	chr1:227071200-227088400	Weak transcription	Hela-S3	cervix
11	chr1:227071200-227091400	Weak transcription	Osteobl	bone
12	chr1:227071400-227084400	Strong transcription	Fetal Intestine Small	intestine
13	chr1:227071600-227087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:227071800-227102400	Weak transcription	Small Intestine	intestine
15	chr1:227072200-227087000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:227072200-227091800	Weak transcription	Fetal Kidney	kidney
17	chr1:227072200-227100400	Weak transcription	Stomach Mucosa	stomach
18	chr1:227072800-227083600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:227073000-227085200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:227073400-227084400	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:227073400-227084600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:227073400-227088600	Strong transcription	Fetal Stomach	stomach
23	chr1:227073400-227092200	Strong transcription	Pancreas	Pancrea
24	chr1:227073800-227100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:227074200-227081800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:227074200-227083000	Strong transcription	Colon Smooth Muscle	Colon
27	chr1:227074200-227091800	Weak transcription	Fetal Heart	heart
28	chr1:227074800-227090000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr1:227074800-227090200	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:227075000-227084200	Strong transcription	Gastric	stomach
31	chr1:227075000-227085400	Strong transcription	Ovary	ovary
32	chr1:227075000-227087400	Weak transcription	Primary B cells from cord blood	blood
33	chr1:227075000-227088800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:227075200-227083200	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr1:227075200-227087000	Weak transcription	GM12878-XiMat	blood
36	chr1:227075200-227091800	Weak transcription	Right Atrium	heart
37	chr1:227075400-227081600	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr1:227075400-227085000	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr1:227075400-227088800	Strong transcription	Liver	Liver
40	chr1:227075600-227083200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:227075600-227083800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:227075600-227088200	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr1:227075800-227084600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:227076400-227082600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:227076400-227083400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:227076400-227084000	Strong transcription	Aorta	Aorta
47	chr1:227076600-227087400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:227077600-227082000	Weak transcription	HepG2	liver
49	chr1:227077800-227085400	Strong transcription	Rectal Smooth Muscle	rectum
50	chr1:227078000-227081800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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