Variant report

Variant	rs6759
Chromosome Location	chr1:227069737-227069738
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	CTCF	chr1:227069700-227069850	GM12871	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227068805..227071011-chr1:227076122..227078773,2	K562	blood:
2	chr1:227067713..227070080-chr1:227071671..227073358,2	K562	blood:

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

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1046240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];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	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11802358	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1295640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs1295641	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	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs2236914	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2236915	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2246221	0.85[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];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	0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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]
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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6759	PSEN2	cis	parietal	SCAN
rs6759	PSEN2	Cis_1M	lymphoblastoid	RTeQTL
rs6759	ARF1	cis	cerebellum	SCAN
rs6759	ZNF74	trans	parietal	SCAN
rs6759	PSEN2	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059600-227070200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:227059800-227070200	Weak transcription	Osteobl	bone
3	chr1:227059800-227075600	Weak transcription	Brain Substantia Nigra	brain
4	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:227060000-227069800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr1:227060000-227070000	Weak transcription	Small Intestine	intestine
7	chr1:227060000-227070600	Weak transcription	Fetal Brain Male	brain
8	chr1:227060200-227070200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:227060400-227073800	Weak transcription	HepG2	liver
10	chr1:227060400-227077600	Weak transcription	Brain Germinal Matrix	brain
11	chr1:227060600-227070400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:227060600-227070400	Weak transcription	HUVEC	blood vessel
13	chr1:227060600-227077400	Weak transcription	Fetal Brain Female	brain
14	chr1:227061200-227069800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr1:227062200-227077400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:227062400-227073000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:227062400-227073000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
19	chr1:227063200-227069800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:227063400-227070200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr1:227063600-227069800	Strong transcription	Fetal Stomach	stomach
22	chr1:227063600-227070200	Weak transcription	Fetal Lung	lung
23	chr1:227063800-227069800	Weak transcription	Colonic Mucosa	Colon
24	chr1:227063800-227070000	Weak transcription	Fetal Kidney	kidney
25	chr1:227063800-227078000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:227064000-227070000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:227064000-227070200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:227064000-227070400	Weak transcription	NH-A	brain
29	chr1:227064000-227072600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:227064200-227069800	Weak transcription	Stomach Mucosa	stomach
31	chr1:227064200-227070600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:227064200-227070600	Weak transcription	Hela-S3	cervix
33	chr1:227064600-227069800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:227064600-227070000	Strong transcription	Fetal Intestine Small	intestine
35	chr1:227064600-227073000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:227065400-227070200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:227065400-227070800	Weak transcription	Brain Anterior Caudate	brain
38	chr1:227065600-227069800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:227065600-227070200	Weak transcription	NHEK	skin
40	chr1:227065800-227077400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:227066200-227069800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:227066200-227072200	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr1:227066400-227069800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:227066600-227069800	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:227066800-227070800	Strong transcription	Aorta	Aorta
46	chr1:227066800-227071400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:227067000-227069800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:227067000-227069800	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:227067000-227070000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:227067000-227070000	Strong transcription	HSMMtube	muscle

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