Variant report

Variant	rs4129816
Chromosome Location	chr1:225769865-225769866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:225769775-225769895	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENAH	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10449249	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10915829	0.85[ASN][1000 genomes]
rs11377355	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12022013	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12026034	0.85[ASN][1000 genomes]
rs12031208	0.85[ASN][1000 genomes]
rs12031651	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12037289	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12038373	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12042273	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12042698	0.82[ASN][1000 genomes]
rs12239415	0.81[ASN][1000 genomes]
rs1340870	0.81[ASN][1000 genomes]
rs1340871	0.85[ASN][1000 genomes]
rs1340872	0.85[ASN][1000 genomes]
rs16845000	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2184778	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185531	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296880	0.87[EUR][1000 genomes]
rs2297747	0.85[ASN][1000 genomes]
rs28620013	0.85[ASN][1000 genomes]
rs3766931	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795443	0.82[ASN][1000 genomes]
rs56169721	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58269599	0.85[ASN][1000 genomes]
rs59912270	0.85[ASN][1000 genomes]
rs61333083	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6674621	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681559	0.85[ASN][1000 genomes]
rs6684314	0.85[ASN][1000 genomes]
rs6684956	0.84[ASN][1000 genomes]
rs6694938	0.82[ASN][1000 genomes]
rs74146931	0.81[ASN][1000 genomes]
rs74146994	0.85[ASN][1000 genomes]
rs74149835	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74149844	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7415548	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7543444	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4129816	LBR	cis	Artery Tibial	GTEx
rs4129816	LBR	cis	Esophagus Muscularis	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
2	chr1:225745000-225770000	Weak transcription	HUVEC	blood vessel
3	chr1:225745000-225772800	Weak transcription	Fetal Brain Female	brain
4	chr1:225748800-225799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:225749200-225783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:225755200-225772200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:225759600-225787600	Weak transcription	Fetal Intestine Small	intestine
8	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:225766400-225780000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:225766400-225783600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:225766600-225779600	Weak transcription	NH-A	brain
12	chr1:225767000-225773600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:225767600-225770800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:225767800-225770400	Enhancers	Colon Smooth Muscle	Colon
15	chr1:225768000-225770000	Enhancers	Fetal Muscle Leg	muscle
16	chr1:225768200-225770600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr1:225768200-225770600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:225768400-225781200	Weak transcription	Right Ventricle	heart
19	chr1:225768600-225770600	Enhancers	A549	lung
20	chr1:225768600-225787800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:225768800-225770000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:225768800-225770600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:225768800-225781000	Weak transcription	HSMM	muscle
24	chr1:225768800-225805600	Weak transcription	Aorta	Aorta
25	chr1:225769000-225770200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:225769000-225774400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:225769000-225783000	Weak transcription	HSMMtube	muscle
28	chr1:225769200-225770000	Weak transcription	Fetal Brain Male	brain
29	chr1:225769200-225770000	Enhancers	Psoas Muscle	Psoas
30	chr1:225769200-225770000	Enhancers	Right Atrium	heart
31	chr1:225769200-225770400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr1:225769200-225770600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:225769200-225770600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr1:225769200-225770600	Enhancers	Stomach Smooth Muscle	stomach
35	chr1:225769200-225773600	Weak transcription	Fetal Stomach	stomach
36	chr1:225769200-225773800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:225769200-225775000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:225769200-225779800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:225769200-225783200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:225769400-225770000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:225769400-225770000	Enhancers	Fetal Muscle Trunk	muscle
42	chr1:225769400-225770000	Enhancers	Left Ventricle	heart
43	chr1:225769400-225770600	Enhancers	Fetal Heart	heart
44	chr1:225769400-225779600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:225769600-225770400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:225769600-225770600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr1:225769800-225770000	Enhancers	Brain Anterior Caudate	brain
48	chr1:225769800-225770000	Genic enhancers	Lung	lung
49	chr1:225769800-225770200	Strong transcription	Fetal Lung	lung
50	chr1:225769800-225770200	Weak transcription	Ovary	ovary

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