Variant report

Variant	rs34230854
Chromosome Location	chr3:53078590-53078591
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53077653..53079153-chr3:53079208..53080925,2	K562	blood:

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11130332	0.88[EUR][1000 genomes]
rs11707576	0.88[EUR][1000 genomes]
rs11708223	0.87[EUR][1000 genomes]
rs13082061	0.86[EUR][1000 genomes]
rs17304995	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255107	0.84[AMR][1000 genomes]
rs2336669	0.86[EUR][1000 genomes]
rs2336671	0.86[EUR][1000 genomes]
rs2564947	0.93[EUR][1000 genomes]
rs2581779	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2581780	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2581796	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2581797	0.88[EUR][1000 genomes]
rs2581801	0.88[EUR][1000 genomes]
rs2581802	0.88[EUR][1000 genomes]
rs2581805	0.87[EUR][1000 genomes]
rs2581810	0.84[EUR][1000 genomes]
rs2581815	0.88[EUR][1000 genomes]
rs2581820	0.90[EUR][1000 genomes]
rs2581823	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2710345	0.88[EUR][1000 genomes]
rs35380116	0.85[EUR][1000 genomes]
rs4519686	0.89[EUR][1000 genomes]
rs4687692	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687699	0.88[EUR][1000 genomes]
rs59989280	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6445550	0.88[EUR][1000 genomes]
rs6768844	0.89[EUR][1000 genomes]
rs6770957	0.90[EUR][1000 genomes]
rs6771610	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6789219	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792578	0.89[EUR][1000 genomes]
rs6805298	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71301803	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71301807	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621939	0.88[EUR][1000 genomes]
rs7637082	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7644973	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648514	0.86[EUR][1000 genomes]
rs7652131	0.90[EUR][1000 genomes]
rs9311485	0.86[EUR][1000 genomes]
rs9812543	0.90[EUR][1000 genomes]
rs9813024	0.85[EUR][1000 genomes]
rs9831409	0.88[EUR][1000 genomes]
rs9842974	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9846976	0.89[EUR][1000 genomes]
rs9847024	0.83[EUR][1000 genomes]
rs9865094	0.86[EUR][1000 genomes]
rs9870898	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1823728	chr3:53046712-53080351	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1820544	chr3:53046712-53096394	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv822094	chr3:53059674-53096460	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv590341	chr3:53077372-53079522	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv590342	chr3:53077372-53079888	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3341503	chr3:53078462-53080760	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs34230854	ITIH4-AS1	cis	Artery Tibial	GTEx
rs34230854	SERBP1P3	cis	lung	GTEx
rs34230854	ITIH4	Cis_1M	lymphoblastoid	RTeQTL
rs34230854	ITIH4-AS1	cis	lung	GTEx
rs34230854	MUSTN1	cis	Artery Aorta	GTEx
rs34230854	ITIH4-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53065400-53078600	Weak transcription	Gastric	stomach
2	chr3:53071000-53078600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:53077400-53079000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr3:53077600-53078600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:53077600-53078600	Flanking Active TSS	GM12878-XiMat	blood
6	chr3:53077600-53078800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr3:53077600-53079000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr3:53077600-53079000	Flanking Active TSS	Dnd41	blood
9	chr3:53077800-53078800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:53077800-53080800	Active TSS	Right Atrium	heart
11	chr3:53078000-53078600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:53078000-53081200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:53078200-53078600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
14	chr3:53078200-53078600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:53078200-53078600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr3:53078200-53078600	Flanking Active TSS	Brain Cingulate Gyrus	brain
17	chr3:53078200-53078600	Flanking Active TSS	Brain Germinal Matrix	brain
18	chr3:53078200-53078600	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr3:53078200-53078600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
20	chr3:53078200-53078600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:53078200-53078600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr3:53078200-53078600	Flanking Active TSS	Fetal Intestine Large	intestine
23	chr3:53078200-53078600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr3:53078200-53078600	Flanking Active TSS	Rectal Smooth Muscle	rectum
25	chr3:53078200-53078600	Flanking Active TSS	A549	lung
26	chr3:53078200-53078600	Enhancers	HSMM	muscle
27	chr3:53078200-53078800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:53078200-53078800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
29	chr3:53078200-53078800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:53078200-53078800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:53078200-53078800	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr3:53078200-53078800	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr3:53078200-53078800	Flanking Active TSS	Fetal Brain Male	brain
34	chr3:53078200-53078800	Flanking Active TSS	Fetal Brain Female	brain
35	chr3:53078200-53078800	Flanking Active TSS	K562	blood
36	chr3:53078200-53079000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:53078200-53079000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr3:53078200-53079000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:53078200-53079000	Flanking Active TSS	Liver	Liver
40	chr3:53078200-53079000	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr3:53078200-53079000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr3:53078200-53079000	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr3:53078200-53079000	Flanking Active TSS	HMEC	breast
44	chr3:53078200-53079000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
45	chr3:53078200-53079000	Flanking Active TSS	NHEK	skin
46	chr3:53078200-53079000	Flanking Active TSS	Osteobl	bone
47	chr3:53078200-53080200	Active TSS	Colonic Mucosa	Colon
48	chr3:53078200-53080800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr3:53078200-53080800	Active TSS	Small Intestine	intestine
50	chr3:53078200-53081200	Active TSS	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links