Variant report

Variant	rs4671860
Chromosome Location	chr2:54341655-54341656
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:54341621-54343455	HepG2	liver:	n/a	n/a
2	MYBL2	chr2:54341649-54343366	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54196743..54198781-chr2:54341566..54344110,2	K562	blood:
2	chr2:54341520..54343821-chr2:54682367..54684141,3	MCF-7	breast:
3	chr2:54341216..54345253-chr2:54347980..54351307,5	MCF-7	breast:
4	chr2:54340617..54344494-chr2:54480899..54484108,3	K562	blood:
5	chr2:54341515..54343973-chr2:55337394..55340042,2	MCF-7	breast:
6	chr2:54341307..54344135-chr2:54557168..54559182,2	K562	blood:
7	chr2:54341443..54343043-chr2:54557751..54559883,2	MCF-7	breast:

No data

Variant related genes	Relation type
ACYP2	TF binding region
ENSG00000068878	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000177994	Chromatin interaction
ENSG00000178021	Chromatin interaction
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10203576	0.80[AMR][1000 genomes]
rs10207537	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1058320	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1075265	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10865279	0.80[ASN][1000 genomes]
rs11125524	0.81[ASN][1000 genomes]
rs11695734	0.85[ASN][1000 genomes]
rs11888384	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11896781	0.80[ASN][1000 genomes]
rs1421622	0.80[AMR][1000 genomes]
rs1833498	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1877906	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2018747	0.85[ASN][1000 genomes]
rs2042143	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2048749	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2112124	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2287642	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2357954	0.89[ASN][1000 genomes]
rs34769118	0.83[ASN][1000 genomes]
rs4671190	0.85[ASN][1000 genomes]
rs4671872	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671889	0.85[EUR][1000 genomes]
rs56001939	0.81[ASN][1000 genomes]
rs62137965	0.83[ASN][1000 genomes]
rs6545384	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6545388	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6741891	0.85[ASN][1000 genomes]
rs7560947	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7562055	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7566894	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7569743	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7573491	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7591194	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7604357	0.85[ASN][1000 genomes]
rs7607066	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs888635	0.84[ASN][1000 genomes]
rs918357	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs929734	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9808326	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[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	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv1851003	chr2:54324701-54372931	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
11	nsv1007731	chr2:54331179-54452329	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
12	nsv535723	chr2:54331179-54452329	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
13	nsv961690	chr2:54339295-54359290	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4671860	ACYP2	cis	Esophagus Muscularis	GTEx
rs4671860	ACYP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:54331200-54342000	Weak transcription	Psoas Muscle	Psoas
3	chr2:54331200-54342400	Weak transcription	Pancreas	Pancrea
4	chr2:54331400-54342200	Weak transcription	Aorta	Aorta
5	chr2:54333800-54341800	Weak transcription	K562	blood
6	chr2:54334800-54341800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:54334800-54342000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:54335600-54341800	Weak transcription	Fetal Heart	heart
9	chr2:54335800-54341800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:54335800-54341800	Weak transcription	HSMM	muscle
11	chr2:54335800-54341800	Weak transcription	HSMMtube	muscle
12	chr2:54335800-54342000	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:54336000-54341800	Weak transcription	Primary B cells from cord blood	blood
14	chr2:54336000-54341800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:54336000-54341800	Weak transcription	Brain Angular Gyrus	brain
16	chr2:54336000-54341800	Weak transcription	Brain Anterior Caudate	brain
17	chr2:54336000-54341800	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:54336000-54341800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:54336000-54341800	Weak transcription	HMEC	breast
20	chr2:54336000-54342000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:54336000-54342000	Weak transcription	NHEK	skin
22	chr2:54341200-54341800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:54341200-54341800	Enhancers	Brain Substantia Nigra	brain
24	chr2:54341200-54342200	Flanking Active TSS	Dnd41	blood
25	chr2:54341400-54341800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:54341400-54341800	Enhancers	Fetal Brain Male	brain
27	chr2:54341400-54342000	Enhancers	HepG2	liver
28	chr2:54341600-54341800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:54341600-54341800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:54341600-54341800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:54341600-54341800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr2:54341600-54341800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:54341600-54341800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr2:54341600-54341800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:54341600-54342000	Enhancers	Liver	Liver
36	chr2:54341600-54342000	Enhancers	Fetal Thymus	thymus
37	chr2:54341600-54342000	Active TSS	Rectal Smooth Muscle	rectum
38	chr2:54341600-54342000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr2:54341600-54342200	Enhancers	Primary T cells fromperipheralblood	blood
40	chr2:54341600-54342200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:54341600-54342200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:54341600-54342400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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