Variant report

Variant	rs6834696
Chromosome Location	chr4:57273611-57273612
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	chr4:57265970..57269312-chr4:57270989..57273638,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10008223	0.95[ASN][1000 genomes]
rs10013402	0.97[ASN][1000 genomes]
rs10017460	0.96[ASN][1000 genomes]
rs10051	0.83[ASN][1000 genomes]
rs10434444	0.98[ASN][1000 genomes]
rs10434445	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10461357	0.85[ASN][1000 genomes]
rs1060472	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11133442	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1124569	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12498340	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12501334	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12501502	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12503412	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12504291	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12505767	0.80[ASN][1000 genomes]
rs12505939	0.83[ASN][1000 genomes]
rs12508008	0.85[ASN][1000 genomes]
rs12509542	0.85[ASN][1000 genomes]
rs12510712	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12511770	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12513091	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12646890	0.85[ASN][1000 genomes]
rs14211	0.83[ASN][1000 genomes]
rs1474179	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1520026	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1520030	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17086696	0.97[ASN][1000 genomes]
rs17086794	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17086832	0.82[ASN][1000 genomes]
rs17086853	0.85[ASN][1000 genomes]
rs1967559	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1983378	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2030366	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2271923	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28510634	0.95[ASN][1000 genomes]
rs28866881	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796541	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4263445	0.88[ASN][1000 genomes]
rs4340842	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4346704	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4493603	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4618376	0.85[ASN][1000 genomes]
rs4864579	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4864580	0.97[ASN][1000 genomes]
rs4864583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864585	0.81[ASN][1000 genomes]
rs4865088	0.88[ASN][1000 genomes]
rs4865089	0.89[ASN][1000 genomes]
rs4865092	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4865103	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4865107	0.85[ASN][1000 genomes]
rs4865108	0.83[ASN][1000 genomes]
rs5010012	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55915354	0.83[ASN][1000 genomes]
rs56040009	0.83[ASN][1000 genomes]
rs56099714	0.85[ASN][1000 genomes]
rs56392224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56887793	0.99[ASN][1000 genomes]
rs58151706	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61032900	0.88[ASN][1000 genomes]
rs6554358	0.83[ASN][1000 genomes]
rs66810706	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66858948	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs66863699	0.85[ASN][1000 genomes]
rs67957495	0.88[ASN][1000 genomes]
rs6820279	0.88[ASN][1000 genomes]
rs6820314	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6821301	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6824893	0.82[ASN][1000 genomes]
rs6829250	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6832797	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6846895	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6849183	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6855041	0.90[EUR][1000 genomes]
rs7664841	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7670991	0.93[ASN][1000 genomes]
rs8340	0.91[ASN][1000 genomes]
rs9799864	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv4347	chr4:57261404-57280595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6834696	SRP72	cis	Adipose Subcutaneous	GTEx
rs6834696	SRP72	cis	Esophagus Mucosa	GTEx
rs6834696	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254200-57273800	Weak transcription	Spleen	Spleen
2	chr4:57254600-57276400	Weak transcription	Psoas Muscle	Psoas
3	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:57254800-57275200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr4:57254800-57275400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr4:57254800-57276400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:57254800-57276400	Weak transcription	Right Ventricle	heart
8	chr4:57254800-57276600	Weak transcription	Left Ventricle	heart
9	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:57255200-57275600	Weak transcription	NHLF	lung
11	chr4:57255200-57276400	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:57255200-57276600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:57255200-57276600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:57255200-57276600	Weak transcription	Brain Substantia Nigra	brain
15	chr4:57255400-57276400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:57255600-57275600	Weak transcription	Fetal Brain Female	brain
17	chr4:57255800-57276600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:57256000-57274200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:57256000-57276400	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:57256200-57276600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:57256400-57276600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:57257600-57274200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:57258400-57274200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:57259000-57274000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:57259400-57275600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:57260200-57274200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:57260800-57274200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:57264000-57274000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:57264200-57274000	Strong transcription	GM12878-XiMat	blood
30	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
31	chr4:57264400-57276400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:57265200-57275600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:57267200-57275600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:57267400-57274800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr4:57267400-57275400	Weak transcription	NHDF-Ad	bronchial
38	chr4:57267600-57275600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr4:57267600-57275600	Weak transcription	Osteobl	bone
40	chr4:57267600-57276000	Weak transcription	Brain Anterior Caudate	brain
41	chr4:57267600-57276200	Weak transcription	HSMM	muscle
42	chr4:57267600-57276400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:57267800-57274200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr4:57267800-57275000	Weak transcription	Fetal Kidney	kidney
45	chr4:57267800-57277600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr4:57267800-57278400	Weak transcription	Placenta	Placenta
47	chr4:57268000-57275600	Weak transcription	NH-A	brain
48	chr4:57268400-57274000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr4:57268400-57274200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr4:57268600-57274000	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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