Variant report

Variant	rs1296171
Chromosome Location	chr1:227059606-227059607
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227058393..227060106-chr1:227070481..227073137,2	MCF-7	breast:
2	chr1:227058010..227060717-chr1:227127922..227130467,2	K562	blood:

Variant related genes	Relation type
ENSG00000163050	Chromatin interaction
ENSG00000143801	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1046240	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150897	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1150900	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11802358	0.81[ASN][1000 genomes]
rs12086302	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12758915	0.89[EUR][1000 genomes]
rs1289395	0.83[EUR][1000 genomes]
rs1289396	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1295638	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1295641	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1295643	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1295647	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1794038	0.90[EUR][1000 genomes]
rs1800674	0.84[EUR][1000 genomes]
rs2073489	0.91[ASN][1000 genomes]
rs2236914	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2236915	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2246221	0.87[EUR][1000 genomes]
rs2793461	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2802268	0.83[ASN][1000 genomes]
rs2855559	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2855560	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2855562	0.84[EUR][1000 genomes]
rs2855564	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4653470	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6426547	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6426548	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6674701	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6688068	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6692729	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6697001	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6697431	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6759	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7514364	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7518926	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7530245	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7530370	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7547071	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8383	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[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	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	esv3381082	chr1:227029266-227059927	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	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
4	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
rs1296171	PSEN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227057800-227059800	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr1:227057800-227060600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:227058600-227059800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr1:227058600-227060000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:227058600-227060000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:227058800-227059800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
7	chr1:227058800-227059800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr1:227058800-227059800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr1:227058800-227060000	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr1:227058800-227060000	Flanking Active TSS	Hela-S3	cervix
11	chr1:227058800-227060000	Flanking Active TSS	HSMM	muscle
12	chr1:227058800-227060200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr1:227059000-227059800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:227059000-227059800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:227059000-227059800	Flanking Active TSS	Colon Smooth Muscle	Colon
16	chr1:227059000-227059800	Flanking Active TSS	Rectal Smooth Muscle	rectum
17	chr1:227059000-227059800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr1:227059000-227059800	Flanking Active TSS	NHLF	lung
19	chr1:227059000-227060000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr1:227059000-227060000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:227059000-227060000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr1:227059000-227060000	Bivalent Enhancer	Fetal Lung	lung
23	chr1:227059000-227060000	Flanking Active TSS	Fetal Muscle Trunk	muscle
24	chr1:227059000-227060000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
25	chr1:227059000-227060000	Enhancers	Small Intestine	intestine
26	chr1:227059000-227060000	Enhancers	Spleen	Spleen
27	chr1:227059000-227060400	Flanking Active TSS	HSMMtube	muscle
28	chr1:227059000-227061800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:227059000-227066800	Weak transcription	Aorta	Aorta
30	chr1:227059200-227059800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:227059200-227059800	Enhancers	Primary B cells from peripheral blood	blood
32	chr1:227059200-227059800	Enhancers	Fetal Intestine Small	intestine
33	chr1:227059200-227059800	Flanking Active TSS	A549	lung
34	chr1:227059200-227060000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:227059200-227060000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:227059200-227060000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:227059200-227060000	Enhancers	Psoas Muscle	Psoas
38	chr1:227059200-227060000	Enhancers	Right Atrium	heart
39	chr1:227059200-227060000	Flanking Active TSS	HepG2	liver
40	chr1:227059200-227060200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:227059200-227060600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:227059200-227060600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:227059200-227060600	Enhancers	Placenta	Placenta
44	chr1:227059200-227060600	Enhancers	Left Ventricle	heart
45	chr1:227059200-227060600	Enhancers	Lung	lung
46	chr1:227059200-227060600	Enhancers	HUVEC	blood vessel
47	chr1:227059200-227061000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:227059200-227063600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:227059200-227069000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:227059400-227059800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell

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