Variant report

Variant	rs12071324
Chromosome Location	chr1:227069874-227069875
allele	C/G
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	POLR2A	chr1:227069811-227071003	GM12892	blood:	n/a	n/a
2	MTA3	chr1:227069790-227071211	GM12878	blood:	n/a	n/a
3	CHD2	chr1:227069840-227070874	GM12878	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: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12057618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069540	0.90[AFR][1000 genomes]
rs6677801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6680042	0.90[AMR][1000 genomes]
rs7537037	0.90[AMR][1000 genomes]
rs7539221	0.90[AMR][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:120 , 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	chr1:227060000-227070000	Weak transcription	Small Intestine	intestine
6	chr1:227060000-227070600	Weak transcription	Fetal Brain Male	brain
7	chr1:227060200-227070200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:227060400-227073800	Weak transcription	HepG2	liver
9	chr1:227060400-227077600	Weak transcription	Brain Germinal Matrix	brain
10	chr1:227060600-227070400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr1:227060600-227070400	Weak transcription	HUVEC	blood vessel
12	chr1:227060600-227077400	Weak transcription	Fetal Brain Female	brain
13	chr1:227062200-227077400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:227062400-227073000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:227062400-227073000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
17	chr1:227063400-227070200	Strong transcription	Stomach Smooth Muscle	stomach
18	chr1:227063600-227070200	Weak transcription	Fetal Lung	lung
19	chr1:227063800-227070000	Weak transcription	Fetal Kidney	kidney
20	chr1:227063800-227078000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:227064000-227070000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:227064000-227070200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:227064000-227070400	Weak transcription	NH-A	brain
24	chr1:227064000-227072600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:227064200-227070600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:227064200-227070600	Weak transcription	Hela-S3	cervix
27	chr1:227064600-227070000	Strong transcription	Fetal Intestine Small	intestine
28	chr1:227064600-227073000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:227065400-227070200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:227065400-227070800	Weak transcription	Brain Anterior Caudate	brain
31	chr1:227065600-227070200	Weak transcription	NHEK	skin
32	chr1:227065800-227077400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:227066200-227072200	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr1:227066800-227070800	Strong transcription	Aorta	Aorta
35	chr1:227066800-227071400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:227067000-227070000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:227067000-227070000	Strong transcription	HSMMtube	muscle
38	chr1:227067000-227070800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:227067000-227071800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:227067000-227072000	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr1:227067000-227081400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:227067200-227070200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:227067200-227070400	Strong transcription	A549	lung
44	chr1:227067200-227072000	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr1:227067600-227071800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:227067800-227075400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:227068000-227070400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr1:227068200-227070000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:227068200-227073400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:227068400-227070000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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