Variant report

Variant	rs55888730
Chromosome Location	chr5:178960437-178960438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178960272..178962115-chr5:178969166..178970829,2	MCF-7	breast:
2	chr5:178958463..178961720-chr5:178975691..178978032,4	MCF-7	breast:
3	chr5:178959529..178962397-chr5:178966368..178968696,2	K562	blood:
4	chr5:178958501..178962397-chr5:178966368..178969379,3	K562	blood:
5	chr5:178958919..178961962-chr5:178962607..178965657,3	K562	blood:

Variant related genes	Relation type
ENSG00000176783	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10069256	0.83[AMR][1000 genomes]
rs2411380	0.80[AMR][1000 genomes]
rs34102807	0.81[AMR][1000 genomes]
rs6869842	0.83[AMR][1000 genomes]
rs6870739	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6889447	0.82[AMR][1000 genomes]
rs7380974	0.82[AMR][1000 genomes]
rs7727647	0.83[AMR][1000 genomes]
rs9286047	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv531996	chr5:178669297-178989687	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv34709	chr5:178720968-178961710	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv2757148	chr5:178720968-178961872	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv34254	chr5:178749394-178961710	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv883260	chr5:178828854-178961710	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv5158	chr5:178946891-178968477	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1022509	chr5:178950829-179002751	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55888730	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178957600-178962400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:178957800-178961400	Weak transcription	K562	blood
3	chr5:178958000-178961000	Weak transcription	Right Atrium	heart
4	chr5:178958000-178961200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:178958000-178961400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr5:178958000-178961400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:178958000-178961400	Weak transcription	Liver	Liver
8	chr5:178958000-178961400	Weak transcription	Thymus	Thymus
9	chr5:178958000-178961600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:178958000-178961800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:178958000-178961800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:178958000-178962200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:178958000-178962200	Weak transcription	Spleen	Spleen
14	chr5:178958000-178962400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr5:178958000-178976800	Weak transcription	Fetal Intestine Small	intestine
16	chr5:178958000-178977000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:178958200-178961200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:178958200-178961400	Weak transcription	HepG2	liver
19	chr5:178958200-178961600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:178958200-178961600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr5:178958200-178963200	Weak transcription	Osteobl	bone
22	chr5:178958400-178961400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr5:178958800-178961400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr5:178958800-178961800	Enhancers	Dnd41	blood
25	chr5:178959600-178960600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:178959600-178961000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:178960000-178960600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr5:178960200-178961000	Enhancers	GM12878-XiMat	blood
29	chr5:178960200-178962400	Enhancers	Primary hematopoietic stem cells	blood
30	chr5:178960400-178961200	Enhancers	Primary B cells from peripheral blood	blood
31	chr5:178960400-178962400	Enhancers	Primary B cells from cord blood	blood

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