Variant report

Variant	rs6821301
Chromosome Location	chr4:57317853-57317854
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57301296..57303911-chr4:57316208..57319458,3	MCF-7	breast:
2	chr4:57309697..57312077-chr4:57315535..57318192,2	MCF-7	breast:
3	chr4:57301960..57303479-chr4:57316742..57319608,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128059	Chromatin interaction
ENSG00000128050	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10008223	0.86[ASN][1000 genomes]
rs10013402	0.88[ASN][1000 genomes]
rs10017460	0.87[ASN][1000 genomes]
rs10051	0.92[ASN][1000 genomes]
rs10434444	0.92[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10434445	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1060472	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11133442	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12498340	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12501334	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12501502	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs12503412	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12504291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12505767	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12505939	0.92[ASN][1000 genomes]
rs12508008	0.84[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12509542	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12510712	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12511770	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12513091	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12646890	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13147900	0.91[JPT][hapmap]
rs1401904	0.90[JPT][hapmap]
rs1401906	0.90[JPT][hapmap]
rs14211	0.84[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1474179	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1520026	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1520030	1.00[CEU][hapmap]
rs17086696	0.82[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs17086794	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17086832	0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs17086853	0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1967559	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1983378	0.92[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2030366	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2271923	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs28510634	0.86[ASN][1000 genomes]
rs28866881	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3796541	0.81[AMR][1000 genomes]
rs3822001	0.81[CEU][hapmap]
rs4340842	0.84[CHB][hapmap];0.90[JPT][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4346704	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4493603	1.00[CEU][hapmap]
rs4618376	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4864579	0.84[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4864580	0.88[ASN][1000 genomes]
rs4864583	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4864585	0.89[ASN][1000 genomes]
rs4865092	0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4865103	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4865107	0.94[ASN][1000 genomes]
rs4865108	0.92[ASN][1000 genomes]
rs5010012	0.92[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55915354	0.92[ASN][1000 genomes]
rs56040009	0.92[ASN][1000 genomes]
rs56099714	0.94[ASN][1000 genomes]
rs56229630	0.86[ASN][1000 genomes]
rs56392224	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56887793	0.90[ASN][1000 genomes]
rs58151706	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58333131	0.85[ASN][1000 genomes]
rs6554345	0.91[JPT][hapmap]
rs6554358	0.84[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs66810706	0.81[AMR][1000 genomes]
rs66858948	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs66863699	0.94[ASN][1000 genomes]
rs6820314	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6824893	0.91[ASN][1000 genomes]
rs6829250	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6832797	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6834696	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6834736	0.90[JPT][hapmap]
rs6849183	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6855041	1.00[CEU][hapmap]
rs7664841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670991	0.84[ASN][1000 genomes]
rs8340	0.91[CHB][hapmap];0.80[JPT][hapmap];0.82[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
rs6821301	SRP72	cis	Esophagus Mucosa	GTEx
rs6821301	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr4:57304200-57318800	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:57304200-57319200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:57304400-57318400	Weak transcription	Psoas Muscle	Psoas
12	chr4:57304400-57318600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:57304400-57319800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:57304400-57320200	Weak transcription	Fetal Heart	heart
15	chr4:57304400-57320200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:57304400-57321200	Weak transcription	HSMMtube	muscle
17	chr4:57304400-57330800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:57304400-57330800	Weak transcription	Brain Substantia Nigra	brain
19	chr4:57304400-57331400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr4:57305800-57330400	Strong transcription	Fetal Thymus	thymus
21	chr4:57306200-57330200	Weak transcription	Brain Angular Gyrus	brain
22	chr4:57306200-57332200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:57306600-57323200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:57306600-57329400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:57306600-57330200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:57306600-57330400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:57306800-57321800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:57306800-57322200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:57306800-57330200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:57306800-57331000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:57307000-57325800	Strong transcription	HMEC	breast
32	chr4:57307000-57326200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr4:57307000-57330000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:57307200-57329600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:57307400-57329000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:57307400-57329400	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr4:57307400-57329400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:57307400-57329400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:57307400-57329600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:57307400-57329800	Strong transcription	K562	blood
41	chr4:57307400-57330800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:57308000-57325800	Weak transcription	Colonic Mucosa	Colon
43	chr4:57308200-57328800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:57308400-57329000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr4:57308800-57318800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr4:57308800-57330000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:57309000-57330600	Weak transcription	Fetal Brain Male	brain
48	chr4:57309200-57321000	Weak transcription	Brain Anterior Caudate	brain
49	chr4:57310000-57319800	Weak transcription	Fetal Lung	lung
50	chr4:57311200-57328800	Strong transcription	Liver	Liver

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