Variant report

Variant	rs4346704
Chromosome Location	chr4:57315998-57315999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:57309697..57312077-chr4:57315535..57318192,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10008223	0.83[ASN][1000 genomes]
rs10013402	0.85[ASN][1000 genomes]
rs10017460	0.84[ASN][1000 genomes]
rs10051	0.89[ASN][1000 genomes]
rs10434444	0.86[ASN][1000 genomes]
rs10434445	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1060472	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11133442	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12498340	0.81[ASN][1000 genomes]
rs12501334	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12501502	0.80[AMR][1000 genomes]
rs12503412	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12504291	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12505767	0.86[ASN][1000 genomes]
rs12505939	0.89[ASN][1000 genomes]
rs12508008	0.91[ASN][1000 genomes]
rs12509542	0.91[ASN][1000 genomes]
rs12510712	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12511770	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12513091	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12646890	0.91[ASN][1000 genomes]
rs14211	0.89[ASN][1000 genomes]
rs1474179	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1520026	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17086696	0.85[ASN][1000 genomes]
rs17086794	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17086832	0.88[ASN][1000 genomes]
rs17086853	0.91[ASN][1000 genomes]
rs1967559	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1983378	0.86[ASN][1000 genomes]
rs2030366	0.86[ASN][1000 genomes]
rs2271923	0.80[AMR][1000 genomes]
rs28510634	0.83[ASN][1000 genomes]
rs28866881	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3796541	0.80[AMR][1000 genomes]
rs4340842	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4618376	0.91[ASN][1000 genomes]
rs4864579	0.85[ASN][1000 genomes]
rs4864580	0.85[ASN][1000 genomes]
rs4864583	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4864585	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4865092	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4865103	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4865107	0.91[ASN][1000 genomes]
rs4865108	0.89[ASN][1000 genomes]
rs5010012	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55915354	0.89[ASN][1000 genomes]
rs56040009	0.89[ASN][1000 genomes]
rs56099714	0.91[ASN][1000 genomes]
rs56229630	0.83[ASN][1000 genomes]
rs56392224	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56887793	0.87[ASN][1000 genomes]
rs58151706	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58333131	0.82[ASN][1000 genomes]
rs6554358	0.89[ASN][1000 genomes]
rs66810706	0.80[AMR][1000 genomes]
rs66858948	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs66863699	0.91[ASN][1000 genomes]
rs6820314	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6821301	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6824893	0.88[ASN][1000 genomes]
rs6829250	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6832797	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6834696	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6849183	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7664841	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7670991	0.81[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4346704	SRP72	cis	Esophagus Mucosa	GTEx
rs4346704	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr4:57304200-57317400	Weak transcription	Thymus	Thymus
9	chr4:57304200-57318800	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:57304200-57319200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:57304400-57317200	Weak transcription	Ovary	ovary
13	chr4:57304400-57317800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:57304400-57318400	Weak transcription	Psoas Muscle	Psoas
15	chr4:57304400-57318600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:57304400-57319800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:57304400-57320200	Weak transcription	Fetal Heart	heart
18	chr4:57304400-57320200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:57304400-57321200	Weak transcription	HSMMtube	muscle
20	chr4:57304400-57330800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:57304400-57330800	Weak transcription	Brain Substantia Nigra	brain
22	chr4:57304400-57331400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr4:57305800-57330400	Strong transcription	Fetal Thymus	thymus
24	chr4:57306200-57330200	Weak transcription	Brain Angular Gyrus	brain
25	chr4:57306200-57332200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:57306600-57323200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:57306600-57329400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:57306600-57330200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:57306600-57330400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:57306800-57316200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:57306800-57321800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:57306800-57322200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:57306800-57330200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:57306800-57331000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:57307000-57325800	Strong transcription	HMEC	breast
36	chr4:57307000-57326200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr4:57307000-57330000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:57307200-57329600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:57307400-57329000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:57307400-57329400	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr4:57307400-57329400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr4:57307400-57329400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:57307400-57329600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:57307400-57329800	Strong transcription	K562	blood
45	chr4:57307400-57330800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:57308000-57325800	Weak transcription	Colonic Mucosa	Colon
47	chr4:57308200-57328800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:57308400-57329000	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr4:57308800-57318800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr4:57308800-57330000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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