Variant report

Variant	rs392907
Chromosome Location	chr5:112153495-112153496
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	chr5:112152202..112156283-chr5:112195630..112198484,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272869	Chromatin interaction
ENSG00000153037	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10463643	0.84[CEU][hapmap]
rs1069061	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs1093677	0.88[CEU][hapmap]
rs1441375	0.96[CEU][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs151976	0.87[CEU][hapmap]
rs151977	0.88[CEU][hapmap]
rs153546	0.84[CEU][hapmap]
rs1661035	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs1661036	0.85[EUR][1000 genomes]
rs1734243	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1816769	0.88[CHB][hapmap]
rs187075	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1966476	0.85[EUR][1000 genomes]
rs1966477	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2229992	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2431238	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2439591	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2464805	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2545159	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545162	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2545163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2545164	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2545165	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2545166	0.88[CEU][hapmap]
rs2545167	0.88[CEU][hapmap]
rs2545169	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2546110	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2546111	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2546116	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2952615	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs351769	0.84[CEU][hapmap]
rs351771	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs372492	0.89[CEU][hapmap]
rs380144	0.81[ASN][1000 genomes]
rs382260	0.88[CEU][hapmap]
rs386830	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs395266	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs397768	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs401908	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41115	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs411356	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs419632	0.85[CEU][hapmap]
rs42427	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs431287	0.89[CEU][hapmap]
rs433429	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs434157	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs438252	0.81[ASN][1000 genomes]
rs448162	0.80[CEU][hapmap]
rs456313	0.85[CEU][hapmap]
rs458967	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs459552	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs463229	0.89[CEU][hapmap]
rs464002	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs464708	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs465454	0.84[CEU][hapmap]
rs465899	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs468179	0.86[EUR][1000 genomes]
rs469760	0.88[CEU][hapmap]
rs495794	0.85[CEU][hapmap]
rs497844	0.80[CEU][hapmap]
rs501250	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs514763	0.84[CEU][hapmap]
rs519397	0.85[CEU][hapmap]
rs529076	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs544243	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs563556	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712668	0.89[CEU][hapmap]
rs7213	0.84[CEU][hapmap]
rs818425	0.85[CEU][hapmap]
rs818427	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs866006	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9011	0.84[CEU][hapmap]

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	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs392907	SRP19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:112103000-112173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112104600-112155400	Weak transcription	Psoas Muscle	Psoas
4	chr5:112118200-112155600	Weak transcription	Right Ventricle	heart
5	chr5:112118200-112177000	Weak transcription	Colonic Mucosa	Colon
6	chr5:112129000-112154600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:112129000-112157400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr5:112129400-112163800	Weak transcription	Small Intestine	intestine
9	chr5:112129600-112163600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:112129800-112154800	Weak transcription	NH-A	brain
11	chr5:112130600-112154800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:112130600-112155400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:112130600-112155600	Weak transcription	Fetal Heart	heart
14	chr5:112130800-112154800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:112130800-112155400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:112131800-112157800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:112131800-112164000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr5:112132000-112154800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:112132000-112174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr5:112132200-112155200	Weak transcription	Fetal Brain Male	brain
21	chr5:112132800-112179800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:112133400-112154800	Weak transcription	HepG2	liver
23	chr5:112133600-112160800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:112133600-112161400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:112134000-112153600	Weak transcription	NHDF-Ad	bronchial
26	chr5:112134000-112162800	Weak transcription	Colon Smooth Muscle	Colon
27	chr5:112136600-112176200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr5:112137000-112154800	Weak transcription	HUVEC	blood vessel
29	chr5:112140400-112183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr5:112141400-112162400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr5:112143600-112159800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:112144200-112159800	Strong transcription	HSMM	muscle
33	chr5:112145400-112165600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:112145600-112156600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:112146200-112165800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr5:112147800-112154600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr5:112147800-112154600	Weak transcription	Esophagus	oesophagus
38	chr5:112147800-112154800	Weak transcription	Brain Germinal Matrix	brain
39	chr5:112147800-112154800	Weak transcription	Fetal Kidney	kidney
40	chr5:112147800-112154800	Weak transcription	HSMMtube	muscle
41	chr5:112147800-112155200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr5:112147800-112155600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr5:112149000-112163600	Weak transcription	A549	lung
44	chr5:112149400-112176400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr5:112149800-112156400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:112149800-112157800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr5:112149800-112159400	Strong transcription	Adipose Nuclei	Adipose
48	chr5:112149800-112159800	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr5:112149800-112166400	Strong transcription	Fetal Thymus	thymus
50	chr5:112150200-112161200	Strong transcription	Primary B cells from cord blood	blood

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