Variant report

Variant	rs4949677
Chromosome Location	chr1:76266662-76266663
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76261350..76264622-chr1:76266576..76269506,4	MCF-7	breast:
2	chr1:76259028..76263655-chr1:76264104..76269438,8	MCF-7	breast:
3	chr1:76256951..76259579-chr1:76264447..76268125,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000057468	Chromatin interaction
ENSG00000137955	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10732723	0.81[CEU][hapmap]
rs10782558	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873788	0.81[CEU][hapmap]
rs11161620	0.91[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161626	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161792	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11161836	0.81[CEU][hapmap]
rs11161857	0.81[CEU][hapmap]
rs1144336	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146646	0.86[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146653	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588578	0.81[CEU][hapmap]
rs1159214	0.85[CEU][hapmap]
rs12021855	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12090849	0.80[CEU][hapmap]
rs12093623	0.91[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094842	0.84[EUR][1000 genomes]
rs12122939	0.91[CEU][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136360	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568447	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12723575	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1565717	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650138	0.91[YRI][hapmap]
rs1770887	0.80[CEU][hapmap]
rs2029681	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2029683	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs2172507	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2172508	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211080	0.86[EUR][1000 genomes]
rs2347962	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28602663	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2881786	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4949879	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4949885	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267813	0.82[EUR][1000 genomes]
rs56352044	0.80[EUR][1000 genomes]
rs5745336	0.91[CEU][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745363	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745381	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5745390	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5745427	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5745433	0.85[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5745442	0.81[CEU][hapmap]
rs61770533	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61799990	0.85[EUR][1000 genomes]
rs6678348	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6683437	0.86[YRI][hapmap]
rs6699682	0.80[CEU][hapmap]
rs7516226	0.81[EUR][1000 genomes]
rs7523573	0.81[CEU][hapmap]
rs7538800	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7547056	0.91[CEU][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549863	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs931507	0.80[CEU][hapmap]
rs9662166	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4949677	MSH4	cis	Esophagus Muscularis	GTEx
rs4949677	ACADM	cis	Whole Blood	GTEx
rs4949677	MSH4	cis	Artery Tibial	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76262400-76267600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:76262400-76267800	Weak transcription	Osteobl	bone
3	chr1:76262400-76269400	Weak transcription	NHDF-Ad	bronchial
4	chr1:76262400-76273200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:76262400-76282800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:76262600-76288800	Weak transcription	Brain Substantia Nigra	brain
7	chr1:76262600-76294600	Weak transcription	Primary B cells from cord blood	blood
8	chr1:76263000-76269400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:76263000-76276600	Weak transcription	Gastric	stomach
10	chr1:76263000-76287400	Weak transcription	Aorta	Aorta
11	chr1:76263000-76289000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:76263000-76296200	Weak transcription	Ovary	ovary
13	chr1:76263200-76266800	Weak transcription	GM12878-XiMat	blood
14	chr1:76263200-76268000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:76263200-76277000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:76263400-76289000	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:76263600-76284000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr1:76263800-76266800	Weak transcription	Fetal Brain Female	brain
19	chr1:76264000-76269400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:76264000-76270600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:76264000-76274200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:76264000-76277000	Weak transcription	HUVEC	blood vessel
23	chr1:76264200-76268600	Weak transcription	NH-A	brain
24	chr1:76264200-76274800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:76264200-76279800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:76264200-76291400	Weak transcription	Psoas Muscle	Psoas
27	chr1:76264600-76267600	Weak transcription	Right Ventricle	heart
28	chr1:76264600-76273600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr1:76264600-76278000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:76264600-76288600	Weak transcription	Left Ventricle	heart
31	chr1:76264800-76277000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:76264800-76288600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:76264800-76288600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:76265200-76266800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:76265600-76270200	Weak transcription	Adipose Nuclei	Adipose
36	chr1:76266000-76272800	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links