Variant report

Variant	rs12747261
Chromosome Location	chr1:227072001-227072002
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	SPI1	chr1:227071852-227072191	GM12878	blood:	n/a	n/a
2	SPI1	chr1:227071873-227072155	GM12891	blood:	n/a	n/a
3	BHLHE40	chr1:227071762-227072109	GM12878	blood:	n/a	n/a
4	SPI1	chr1:227071891-227072251	GM12891	blood:	n/a	n/a
5	SPI1	chr1:227071944-227072098	GM12878	blood:	n/a	n/a
6	SPI1	chr1:227071780-227072260	HL-60	blood:	n/a	n/a
7	RFX5	chr1:227071933-227072007	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227067713..227070080-chr1:227071671..227073358,2	K562	blood:
2	chr1:227071996..227075968-chr1:227085768..227088327,4	K562	blood:
3	chr1:227058393..227060106-chr1:227070481..227073137,2	MCF-7	breast:

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

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10799367	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916057	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10916059	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11580744	0.92[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	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12123818	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12125811	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12127440	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12130732	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12138310	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12143886	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12403248	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12405779	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12733650	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12760155	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846644	0.98[EUR][1000 genomes]
rs1800672	0.99[EUR][1000 genomes]
rs1800673	0.99[EUR][1000 genomes]
rs1800681	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236912	0.96[EUR][1000 genomes]
rs3213436	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34081886	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35029375	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35213802	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35244407	0.82[EUR][1000 genomes]
rs35396772	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35519961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35744376	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3820649	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829979	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6426554	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6676065	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6676067	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6680780	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71648404	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs732479	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512804	0.92[EUR][1000 genomes];0.85[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:118 , 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	chr1:227060400-227073800	Weak transcription	HepG2	liver
4	chr1:227060400-227077600	Weak transcription	Brain Germinal Matrix	brain
5	chr1:227060600-227077400	Weak transcription	Fetal Brain Female	brain
6	chr1:227062200-227077400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:227062400-227073000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:227062400-227073000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
10	chr1:227063800-227078000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:227064000-227072600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:227064600-227073000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:227065800-227077400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:227066200-227072200	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr1:227067000-227081400	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:227067800-227075400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:227068200-227073400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:227068600-227074200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:227068800-227072800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:227069400-227074400	Enhancers	Fetal Thymus	thymus
21	chr1:227069400-227076000	Weak transcription	Brain Angular Gyrus	brain
22	chr1:227069400-227085000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:227069400-227087800	Weak transcription	HMEC	breast
24	chr1:227069400-227102800	Weak transcription	K562	blood
25	chr1:227069600-227075000	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr1:227069800-227072200	Enhancers	Stomach Mucosa	stomach
27	chr1:227069800-227074600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:227069800-227075000	Enhancers	Primary hematopoietic stem cells	blood
29	chr1:227069800-227075000	Genic enhancers	Fetal Muscle Leg	muscle
30	chr1:227070000-227072200	Enhancers	Fetal Kidney	kidney
31	chr1:227070000-227076400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:227070000-227079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:227070400-227073400	Enhancers	HUVEC	blood vessel
34	chr1:227070400-227079000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr1:227070600-227073000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:227070600-227073000	Enhancers	Spleen	Spleen
37	chr1:227070600-227075000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
38	chr1:227070800-227073000	Weak transcription	HSMMtube	muscle
39	chr1:227070800-227074000	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:227070800-227075200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:227070800-227088200	Weak transcription	Fetal Brain Male	brain
42	chr1:227071000-227072800	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr1:227071000-227073000	Enhancers	Adipose Nuclei	Adipose
44	chr1:227071000-227073000	Enhancers	Liver	Liver
45	chr1:227071000-227073200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:227071000-227073200	Weak transcription	Ovary	ovary
47	chr1:227071000-227073200	Enhancers	Thymus	Thymus
48	chr1:227071000-227073400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr1:227071000-227073800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:227071000-227074000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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