Variant report

Variant	rs1144336
Chromosome Location	chr1:76277421-76277422
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76277185..76279387-chr1:76282606..76285233,2	K562	blood:
2	chr1:76259303..76263920-chr1:76276444..76279468,6	K562	blood:
3	chr1:76252079..76256078-chr1:76276265..76280067,4	K562	blood:

Variant related genes	Relation type
ENSG00000207241	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000201487	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000057468	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10782558	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161620	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161626	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161792	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1146646	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146653	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12021855	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12093623	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094842	0.82[EUR][1000 genomes]
rs12122939	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127078	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136360	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568447	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12723575	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1565717	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029681	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2029683	0.82[EUR][1000 genomes]
rs2172507	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2172508	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211080	0.84[EUR][1000 genomes]
rs2347962	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2881786	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4949677	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949885	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267813	0.80[EUR][1000 genomes]
rs5745336	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745363	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745381	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5745390	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs5745427	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5745433	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61770533	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61799990	0.83[EUR][1000 genomes]
rs6678348	0.85[EUR][1000 genomes]
rs7538800	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7547056	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549863	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1795237	chr1:76268573-76383565	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1800125	chr1:76269439-76379497	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1799260	chr1:76269439-76383297	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1847721	chr1:76269439-76383565	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1144336	MSH4	cis	Artery Tibial	GTEx
rs1144336	MSH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76262400-76282800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr1:76262600-76288800	Weak transcription	Brain Substantia Nigra	brain
3	chr1:76262600-76294600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:76263000-76287400	Weak transcription	Aorta	Aorta
5	chr1:76263000-76289000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:76263000-76296200	Weak transcription	Ovary	ovary
7	chr1:76263400-76289000	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:76263600-76284000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:76264200-76279800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:76264200-76291400	Weak transcription	Psoas Muscle	Psoas
11	chr1:76264600-76278000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:76264600-76288600	Weak transcription	Left Ventricle	heart
13	chr1:76264800-76288600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:76264800-76288600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:76277000-76277800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:76277000-76278000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr1:76277000-76278000	Enhancers	Stomach Mucosa	stomach
18	chr1:76277000-76278000	Enhancers	HUVEC	blood vessel
19	chr1:76277200-76277600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:76277200-76277600	Enhancers	NH-A	brain
21	chr1:76277200-76278000	Enhancers	Osteobl	bone
22	chr1:76277400-76278200	Enhancers	HepG2	liver
23	chr1:76277400-76278800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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