Variant report

Variant	rs56071539
Chromosome Location	chr5:179010119-179010120
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	chr5:179008184..179011132-chr5:179049089..179051840,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169045	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10054335	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10056863	0.96[ASN][1000 genomes]
rs10479543	0.85[EUR][1000 genomes]
rs11249649	0.86[ASN][1000 genomes]
rs12719865	0.95[ASN][1000 genomes]
rs13183244	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28639796	0.95[ASN][1000 genomes]
rs34316961	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4256313	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4701143	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62397276	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601054	0.97[ASN][1000 genomes]
rs6895677	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7448707	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7706275	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	esv2758031	chr5:178661266-179037529	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv2759397	chr5:178661266-179037529	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
5	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
6	nsv883269	chr5:178951106-179031595	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
8	nsv1015477	chr5:178954409-179016804	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv883271	chr5:178955046-179031595	Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv883272	chr5:178961872-179031595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1028236	chr5:178962087-179019981	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56071539	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178987200-179040800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:178987400-179013200	Strong transcription	Fetal Stomach	stomach
3	chr5:178987400-179019800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:178987600-179045600	Strong transcription	Fetal Intestine Small	intestine
5	chr5:178987800-179012200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:178987800-179017000	Strong transcription	Osteobl	bone
7	chr5:178987800-179031000	Strong transcription	Fetal Muscle Leg	muscle
8	chr5:178987800-179045600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:178988400-179010200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:178989000-179010200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr5:178991200-179016600	Weak transcription	Stomach Mucosa	stomach
12	chr5:178996200-179022600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:178996600-179013200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:178996800-179034000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr5:178997600-179012800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr5:178997600-179020200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:178998400-179012800	Weak transcription	HSMM	muscle
18	chr5:178999400-179012800	Weak transcription	HMEC	breast
19	chr5:178999800-179013000	Weak transcription	Brain Substantia Nigra	brain
20	chr5:178999800-179013800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr5:178999800-179034800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:179000000-179013000	Weak transcription	Psoas Muscle	Psoas
23	chr5:179000000-179034200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:179000400-179022800	Weak transcription	Fetal Heart	heart
25	chr5:179002200-179017000	Strong transcription	Brain Germinal Matrix	brain
26	chr5:179002200-179022800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:179002200-179045600	Strong transcription	Fetal Intestine Large	intestine
28	chr5:179002600-179013200	Weak transcription	K562	blood
29	chr5:179002800-179012400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:179002800-179012600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:179002800-179012800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr5:179002800-179012800	Weak transcription	GM12878-XiMat	blood
33	chr5:179003000-179012400	Weak transcription	Esophagus	oesophagus
34	chr5:179003200-179013000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:179003200-179015200	Weak transcription	Fetal Brain Male	brain
36	chr5:179003200-179016400	Weak transcription	HSMMtube	muscle
37	chr5:179003400-179012600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr5:179003400-179012800	Weak transcription	Brain Angular Gyrus	brain
39	chr5:179003400-179013000	Weak transcription	Small Intestine	intestine
40	chr5:179004000-179013600	Weak transcription	NHDF-Ad	bronchial
41	chr5:179004800-179011800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:179004800-179012000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:179004800-179013200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr5:179005000-179032400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr5:179005400-179010200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:179006000-179013000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr5:179006200-179012800	Weak transcription	NHLF	lung
48	chr5:179006200-179019600	Weak transcription	Hela-S3	cervix
49	chr5:179006800-179012800	Weak transcription	Spleen	Spleen
50	chr5:179007400-179010200	Strong transcription	Duodenum Smooth Muscle	Duodenum

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