Variant report

Variant	rs12069540
Chromosome Location	chr1:227074002-227074003
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	IKZF1	chr1:227073837-227074053	GM12878	blood:	n/a	n/a
2	MEF2A	chr1:227073840-227074143	GM12878	blood:	n/a	chr1:227074018-227074033 chr1:227073975-227073996 chr1:227073977-227073991 chr1:227074018-227074032 chr1:227074017-227074032 chr1:227074017-227074032 chr1:227074020-227074031 chr1:227074016-227074037 chr1:227074021-227074030 chr1:227074016-227074037 chr1:227074017-227074033

No.	Distal block	Cell Line	Cell type
1	chr1:227073623..227075968-chr1:227085768..227087607,2	K562	blood:
2	chr1:227072686..227076463-chr1:227077857..227081301,5	K562	blood:
3	chr1:227072686..227075297-chr1:227079508..227082129,3	K562	blood:
4	chr1:227071996..227075968-chr1:227085768..227088327,4	K562	blood:
5	chr1:227061527..227064235-chr1:227072734..227074353,2	K562	blood:

Variant related genes	Relation type
PSEN2	TF binding region
ENSG00000163050	Chromatin interaction
ENSG00000143801	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12057618	0.90[AFR][1000 genomes]
rs12071324	0.90[AFR][1000 genomes]
rs16846590	0.93[ASN][1000 genomes]
rs58698650	0.93[ASN][1000 genomes]
rs61185121	0.93[ASN][1000 genomes]
rs6671059	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6675452	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6677801	0.90[AFR][1000 genomes]
rs6677908	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6678839	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6678940	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7522645	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7523790	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7525819	0.92[AMR][1000 genomes];0.93[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

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059800-227075600	Weak transcription	Brain Substantia Nigra	brain
2	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:227060400-227077600	Weak transcription	Brain Germinal Matrix	brain
4	chr1:227060600-227077400	Weak transcription	Fetal Brain Female	brain
5	chr1:227062200-227077400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
7	chr1:227063800-227078000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:227065800-227077400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:227067000-227081400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:227067800-227075400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:227068600-227074200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:227069400-227074400	Enhancers	Fetal Thymus	thymus
13	chr1:227069400-227076000	Weak transcription	Brain Angular Gyrus	brain
14	chr1:227069400-227085000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:227069400-227087800	Weak transcription	HMEC	breast
16	chr1:227069400-227102800	Weak transcription	K562	blood
17	chr1:227069600-227075000	Genic enhancers	Fetal Muscle Trunk	muscle
18	chr1:227069800-227074600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr1:227069800-227075000	Enhancers	Primary hematopoietic stem cells	blood
20	chr1:227069800-227075000	Genic enhancers	Fetal Muscle Leg	muscle
21	chr1:227070000-227076400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:227070000-227079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:227070400-227079000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:227070600-227075000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:227070800-227075200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:227070800-227088200	Weak transcription	Fetal Brain Male	brain
27	chr1:227071000-227074200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:227071000-227074200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:227071000-227074200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:227071000-227074400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr1:227071000-227074600	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr1:227071000-227074800	Enhancers	Primary B cells from peripheral blood	blood
33	chr1:227071000-227076000	Weak transcription	NHEK	skin
34	chr1:227071000-227077400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:227071000-227089000	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:227071200-227074200	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:227071200-227074400	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr1:227071200-227075200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:227071200-227075400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:227071200-227075600	Weak transcription	Fetal Intestine Large	intestine
41	chr1:227071200-227075600	Genic enhancers	Lung	lung
42	chr1:227071200-227076000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:227071200-227086800	Weak transcription	NHDF-Ad	bronchial
44	chr1:227071200-227088400	Weak transcription	Hela-S3	cervix
45	chr1:227071200-227091400	Weak transcription	Osteobl	bone
46	chr1:227071400-227075000	Enhancers	Primary B cells from cord blood	blood
47	chr1:227071400-227076200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:227071400-227079000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:227071400-227079600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:227071400-227080000	Weak transcription	Muscle Satellite Cultured Cells	--

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