Variant report

Variant	rs732479
Chromosome Location	chr1:227065478-227065479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:227065451-227065544	NB4	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227063913..227065661-chr1:227075217..227077074,2	MCF-7	breast:
2	chr1:226830168..226832886-chr1:227064468..227067080,2	K562	blood:
3	chr1:227063874..227066086-chr1:227080166..227082122,2	K562	blood:
4	chr1:227064075..227066855-chr1:227067871..227070259,4	MCF-7	breast:
5	chr1:227063887..227066680-chr1:227122260..227124831,2	K562	blood:

No data

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

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10799367	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916057	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10916059	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11580744	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11588886	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119853	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12123818	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12125811	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12127440	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12130732	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12132893	0.93[JPT][hapmap]
rs12138310	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12143886	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12403248	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12405779	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12733650	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12747261	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760155	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846644	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1794035	0.82[CEU][hapmap]
rs1800672	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1800673	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1800681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236912	0.94[EUR][1000 genomes]
rs3213436	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]
rs34081886	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35029375	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35213802	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35244407	0.83[EUR][1000 genomes]
rs35396772	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35519961	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35744376	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3820649	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829979	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426554	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6676065	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6676067	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]
rs6680780	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71648404	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7512804	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[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

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059000-227066800	Weak transcription	Aorta	Aorta
2	chr1:227059200-227069000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:227059400-227069600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:227059600-227066000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:227059600-227068400	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:227059600-227069200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:227059600-227070200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:227059800-227067400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:227059800-227070200	Weak transcription	Osteobl	bone
10	chr1:227059800-227075600	Weak transcription	Brain Substantia Nigra	brain
11	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:227060000-227068200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:227060000-227068200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:227060000-227068400	Weak transcription	Brain Angular Gyrus	brain
15	chr1:227060000-227068800	Weak transcription	NHDF-Ad	bronchial
16	chr1:227060000-227069400	Weak transcription	Esophagus	oesophagus
17	chr1:227060000-227069600	Weak transcription	Right Atrium	heart
18	chr1:227060000-227069800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:227060000-227070000	Weak transcription	Small Intestine	intestine
20	chr1:227060000-227070600	Weak transcription	Fetal Brain Male	brain
21	chr1:227060200-227070200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:227060400-227066200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:227060400-227067000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr1:227060400-227068400	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:227060400-227069200	Weak transcription	GM12878-XiMat	blood
26	chr1:227060400-227073800	Weak transcription	HepG2	liver
27	chr1:227060400-227077600	Weak transcription	Brain Germinal Matrix	brain
28	chr1:227060600-227067200	Weak transcription	Ovary	ovary
29	chr1:227060600-227067400	Weak transcription	NHLF	lung
30	chr1:227060600-227068400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:227060600-227070400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:227060600-227070400	Weak transcription	HUVEC	blood vessel
33	chr1:227060600-227077400	Weak transcription	Fetal Brain Female	brain
34	chr1:227061200-227069800	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr1:227062000-227065800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:227062000-227067000	Weak transcription	HSMMtube	muscle
37	chr1:227062200-227077400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:227062400-227066200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr1:227062400-227073000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr1:227062400-227073000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:227062600-227066600	Genic enhancers	Fetal Muscle Leg	muscle
42	chr1:227062800-227068400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
44	chr1:227063200-227066400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:227063200-227067200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr1:227063200-227067200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:227063200-227069800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:227063400-227065600	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:227063400-227065800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:227063400-227070200	Strong transcription	Stomach Smooth Muscle	stomach

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