Variant report

Variant	rs10009543
Chromosome Location	chr4:57323951-57323952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57310825..57312727-chr4:57322119..57324286,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10007967	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10015221	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015634	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10518	0.91[ASN][1000 genomes]
rs10866433	0.98[ASN][1000 genomes]
rs12646703	0.92[EUR][1000 genomes]
rs1356787	0.87[EUR][1000 genomes]
rs17086803	0.98[ASN][1000 genomes]
rs28472763	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4073691	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4383672	0.88[EUR][1000 genomes]
rs4524447	0.88[EUR][1000 genomes]
rs4616819	0.88[EUR][1000 genomes]
rs4865102	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4865104	0.98[ASN][1000 genomes]
rs58975286	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6584	0.92[EUR][1000 genomes]
rs6811821	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6816218	0.93[ASN][1000 genomes]
rs6816268	0.89[EUR][1000 genomes]
rs6818715	0.92[EUR][1000 genomes]
rs6819534	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6830518	0.87[EUR][1000 genomes]
rs6842307	0.92[EUR][1000 genomes]
rs6843587	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7692073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7694047	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7700034	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9312675	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10009543	SRP72	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57303400-57330800	Weak transcription	Spleen	Spleen
2	chr4:57303800-57326000	Weak transcription	Gastric	stomach
3	chr4:57303800-57331000	Weak transcription	Stomach Mucosa	stomach
4	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
5	chr4:57304000-57330000	Weak transcription	Pancreas	Pancrea
6	chr4:57304000-57330000	Weak transcription	Right Ventricle	heart
7	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
8	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:57304400-57330800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:57304400-57330800	Weak transcription	Brain Substantia Nigra	brain
11	chr4:57304400-57331400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr4:57305800-57330400	Strong transcription	Fetal Thymus	thymus
13	chr4:57306200-57330200	Weak transcription	Brain Angular Gyrus	brain
14	chr4:57306200-57332200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:57306600-57329400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:57306600-57330200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:57306600-57330400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:57306800-57330200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:57306800-57331000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:57307000-57325800	Strong transcription	HMEC	breast
21	chr4:57307000-57326200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:57307000-57330000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:57307200-57329600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr4:57307400-57329000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:57307400-57329400	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr4:57307400-57329400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:57307400-57329400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr4:57307400-57329600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:57307400-57329800	Strong transcription	K562	blood
30	chr4:57307400-57330800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:57308000-57325800	Weak transcription	Colonic Mucosa	Colon
32	chr4:57308200-57328800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:57308400-57329000	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr4:57308800-57330000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:57309000-57330600	Weak transcription	Fetal Brain Male	brain
36	chr4:57311200-57328800	Strong transcription	Liver	Liver
37	chr4:57311400-57328000	Strong transcription	Dnd41	blood
38	chr4:57313400-57327000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr4:57313800-57329400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:57314000-57326800	Strong transcription	Fetal Muscle Leg	muscle
41	chr4:57314000-57327000	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr4:57314000-57329200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:57314000-57330600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr4:57314400-57329200	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr4:57314600-57325800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:57314600-57328800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr4:57314600-57328800	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:57314600-57328800	Strong transcription	HepG2	liver
49	chr4:57314600-57329000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr4:57314600-57329000	Strong transcription	Duodenum Mucosa	Duodenum

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