Variant report

Variant	rs71628699
Chromosome Location	chr1:155944626-155944627
allele	A/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	REST	chr1:155944316-155949059	H1-neurons	neurons:	n/a	chr1:155948423-155948436 chr1:155947302-155947315 chr1:155948473-155948486 chr1:155947032-155947040 chr1:155948493-155948506
2	POLR2A	chr1:155943560-155949842	HL-60	blood:	n/a	n/a
3	WRNIP1	chr1:155944396-155944692	GM12878	blood:	n/a	n/a
4	MAZ	chr1:155944495-155949843	IMR90	lung:	n/a	chr1:155944774-155944784 chr1:155945544-155945554
5	POLR2A	chr1:155944334-155946388	GM12892	blood:	n/a	n/a
6	MAZ	chr1:155944624-155944846	GM12878	blood:	n/a	chr1:155944774-155944784
7	POLR2A	chr1:155943832-155953868	U87	brain:	n/a	n/a
8	POLR2A	chr1:155944417-155944845	K562	blood:	n/a	n/a
9	POLR2A	chr1:155943838-155953803	U87	brain:	n/a	n/a
10	ELF1	chr1:155944492-155944987	GM12878	blood:	n/a	chr1:155944804-155944815
11	POLR2A	chr1:155943861-155950165	GM12878	blood:	n/a	n/a
12	MTA3	chr1:155943968-155951505	GM12878	blood:	n/a	n/a
13	STAT5A	chr1:155944168-155945223	GM12878	blood:	n/a	chr1:155944894-155944901 chr1:155944776-155944788 chr1:155944581-155944593 chr1:155944770-155944782
14	EBF1	chr1:155944546-155944843	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155943579..155945946-chr1:155950039..155953037,2	MCF-7	breast:
2	chr1:155944222..155946340-chr1:156050353..156052313,2	K562	blood:
3	chr1:155908945..155912358-chr1:155944278..155947594,3	MCF-7	breast:
4	chr1:155944622..155946767-chr1:156092062..156094362,2	MCF-7	breast:
5	chr1:155943593..155946344-chr1:155989264..155990773,2	K562	blood:

Variant related genes	Relation type
ENSG00000273002	TF binding region
ARHGEF2	TF binding region
ENSG00000160789	Chromatin interaction
ENSG00000163479	Chromatin interaction
ENSG00000254726	Chromatin interaction
ENSG00000173080	Chromatin interaction

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

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

rs_ID	r²[population]
rs1010033	0.86[EUR][1000 genomes]
rs1018730	0.86[EUR][1000 genomes]
rs1055184	0.85[EUR][1000 genomes]
rs10908485	0.84[EUR][1000 genomes]
rs12039053	0.86[EUR][1000 genomes]
rs12138833	0.86[EUR][1000 genomes]
rs12747344	0.85[EUR][1000 genomes]
rs1749409	0.85[EUR][1000 genomes]
rs1765275	0.84[EUR][1000 genomes]
rs1964951	0.88[EUR][1000 genomes]
rs2275079	0.85[EUR][1000 genomes]
rs2275081	0.85[EUR][1000 genomes]
rs2364402	0.86[EUR][1000 genomes]
rs2364404	0.86[EUR][1000 genomes]
rs28379575	0.85[EUR][1000 genomes]
rs2886069	0.86[EUR][1000 genomes]
rs34802187	0.85[EUR][1000 genomes]
rs35138477	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35374730	0.83[EUR][1000 genomes]
rs35588936	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35730001	0.88[EUR][1000 genomes]
rs3768280	0.85[EUR][1000 genomes]
rs4412586	0.85[EUR][1000 genomes]
rs4661160	0.86[EUR][1000 genomes]
rs4661162	0.86[EUR][1000 genomes]
rs4661170	0.85[EUR][1000 genomes]
rs4661172	0.86[EUR][1000 genomes]
rs493446	0.85[EUR][1000 genomes]
rs506688	0.85[EUR][1000 genomes]
rs527113	0.85[EUR][1000 genomes]
rs536870	0.85[EUR][1000 genomes]
rs572609	0.85[EUR][1000 genomes]
rs605025	0.84[EUR][1000 genomes]
rs6660802	0.85[EUR][1000 genomes]
rs6667096	0.85[EUR][1000 genomes]
rs708614	0.85[EUR][1000 genomes]
rs71628697	0.84[EUR][1000 genomes]
rs822503	0.84[EUR][1000 genomes]
rs822653	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155905000-155945600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:155935000-155944800	Enhancers	Fetal Heart	heart
3	chr1:155941000-155944800	Enhancers	HUVEC	blood vessel
4	chr1:155941000-155945000	Weak transcription	Pancreas	Pancrea
5	chr1:155941600-155945000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:155941800-155944800	Genic enhancers	Dnd41	blood
7	chr1:155941800-155945200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:155941800-155945400	Enhancers	Psoas Muscle	Psoas
9	chr1:155942000-155944800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
10	chr1:155942800-155945000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:155943000-155945000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:155943000-155945400	Enhancers	Placenta	Placenta
13	chr1:155943000-155947400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:155943600-155944800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
15	chr1:155943600-155945000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr1:155943600-155945000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr1:155943600-155945000	Genic enhancers	Fetal Intestine Small	intestine
18	chr1:155943600-155945200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
19	chr1:155943600-155945200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
20	chr1:155943600-155945200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:155943600-155945200	Flanking Active TSS	Fetal Brain Female	brain
22	chr1:155943600-155945600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:155943600-155945600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:155943600-155945800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:155943600-155947200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr1:155943600-155951400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:155943800-155944800	Genic enhancers	HepG2	liver
28	chr1:155943800-155946000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr1:155944000-155944800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr1:155944000-155944800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:155944000-155944800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr1:155944000-155945000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr1:155944000-155945000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
34	chr1:155944000-155945000	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr1:155944000-155945200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:155944000-155945200	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr1:155944000-155945200	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr1:155944000-155945600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:155944000-155945800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:155944000-155945800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
41	chr1:155944000-155945800	Enhancers	Ovary	ovary
42	chr1:155944000-155946000	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
43	chr1:155944000-155946000	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr1:155944000-155946000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr1:155944000-155946200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr1:155944000-155946200	Flanking Active TSS	HMEC	breast
47	chr1:155944000-155946800	Enhancers	Stomach Mucosa	stomach
48	chr1:155944000-155947200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:155944000-155947600	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr1:155944000-155947600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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