Variant report

Variant	rs12652495
Chromosome Location	chr5:178981301-178981302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:178979685..178981544-chr5:178981841..178984975,3	K562	blood:
2	chr5:178975440..178984076-chr5:179047224..179053131,17	K562	blood:
3	chr5:178979685..178981490-chr5:178983248..178984975,2	K562	blood:
4	chr5:178979256..178982161-chr5:178989561..178991785,2	K562	blood:
5	chr5:178980836..178983768-chr5:179095589..179098241,2	MCF-7	breast:
6	chr5:178975871..178983601-chr5:179047224..179052413,15	K562	blood:
7	chr5:178978852..178982589-chr5:179047122..179052388,6	MCF-7	breast:
8	chr5:178976021..178979527-chr5:178979544..178984972,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000169045	Chromatin interaction
ENSG00000176783	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10064596	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10074573	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10078712	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10078796	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10479541	0.86[AFR][1000 genomes]
rs10479542	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12658664	0.82[EUR][1000 genomes]
rs12658811	0.90[AFR][1000 genomes]
rs13179470	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13183521	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4700835	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4700836	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4701130	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4701131	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4701132	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6601050	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6895321	0.80[EUR][1000 genomes]
rs6896112	0.87[ASN][1000 genomes]
rs6896940	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7702303	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7703730	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7704349	0.81[EUR][1000 genomes]
rs7718673	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7723230	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7733389	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7736163	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
rs12652495	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178978600-178981400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr5:178978600-178981600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:178978600-178986000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:178978800-178981800	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr5:178978800-178985600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:178978800-178985600	Weak transcription	Fetal Brain Female	brain
7	chr5:178978800-178986000	Weak transcription	Aorta	Aorta
8	chr5:178978800-178986200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:178979000-178981400	Enhancers	Esophagus	oesophagus
10	chr5:178979000-178981600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:178979000-178981600	Enhancers	NH-A	brain
12	chr5:178979000-178985600	Weak transcription	HSMM	muscle
13	chr5:178979200-178981400	Enhancers	Spleen	Spleen
14	chr5:178979200-178981600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:178979200-178981600	Enhancers	HUVEC	blood vessel
16	chr5:178979400-178985600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:178979600-178981400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr5:178979600-178981400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:178979600-178981600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:178979600-178981600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr5:178979600-178981600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:178979600-178984800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:178979600-178984800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:178979600-178985600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:178979600-178985600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:178979600-178985800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:178979600-178986000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:178979800-178981400	Enhancers	Hela-S3	cervix
29	chr5:178979800-178981600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:178979800-178981600	Strong transcription	Fetal Stomach	stomach
31	chr5:178979800-178986000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:178980000-178981400	Strong transcription	Fetal Intestine Large	intestine
33	chr5:178980000-178982400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr5:178980000-178985600	Weak transcription	Primary T cells from cord blood	blood
35	chr5:178980000-178985800	Weak transcription	Brain Anterior Caudate	brain
36	chr5:178980000-178985800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr5:178980200-178981400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
38	chr5:178980200-178981400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr5:178980200-178983800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:178980200-178985000	Weak transcription	Liver	Liver
41	chr5:178980200-178985600	Weak transcription	Fetal Lung	lung
42	chr5:178980200-178985600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr5:178980200-178985800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr5:178980400-178981800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:178980400-178982000	Weak transcription	Small Intestine	intestine
46	chr5:178980400-178982600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr5:178980400-178984600	Weak transcription	GM12878-XiMat	blood
48	chr5:178980400-178985400	Weak transcription	Fetal Brain Male	brain
49	chr5:178980400-178985600	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr5:178980400-178985600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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