Variant report

Variant	rs7307562
Chromosome Location	chr12:40724960-40724961
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1019709	0.81[JPT][hapmap]
rs10459265	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10467144	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10467146	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs10735931	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10735934	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10748029	0.82[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs10748030	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10748033	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10748034	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10784470	0.84[CHB][hapmap]
rs10784486	0.84[CHD][hapmap]
rs10784501	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10784503	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10784504	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10784506	0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10784509	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10784548	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs10784595	0.86[JPT][hapmap]
rs10784596	0.86[JPT][hapmap]
rs10878358	0.91[ASN][1000 genomes]
rs10878368	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10878371	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10878377	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs10878405	0.84[CHB][hapmap]
rs10878441	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs11175862	0.89[CHB][hapmap]
rs11176013	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11176030	0.90[CHB][hapmap]
rs11176495	0.86[JPT][hapmap]
rs11564148	0.90[CHB][hapmap]
rs12146857	0.84[CHB][hapmap]
rs12367542	0.90[CHB][hapmap]
rs12426362	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1427263	0.84[CHD][hapmap];0.84[ASN][1000 genomes]
rs1427264	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1427265	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1427266	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1427267	0.81[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs17444124	0.84[CHB][hapmap]
rs17466605	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs1820544	0.86[JPT][hapmap]
rs1820545	0.86[JPT][hapmap]
rs1896252	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1896253	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs1896254	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2069228	0.81[CHB][hapmap]
rs2081701	0.81[JPT][hapmap]
rs2114568	0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2114569	0.85[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2162469	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2404840	0.86[JPT][hapmap]
rs2896975	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs2896982	0.81[JPT][hapmap]
rs3761863	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs3886747	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs4767969	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4767973	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs4768224	0.84[CHD][hapmap]
rs4768227	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4768229	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4768230	0.90[CHB][hapmap]
rs4768236	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs4768237	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs6581667	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6581668	0.84[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7134408	0.84[CHB][hapmap]
rs7137160	0.90[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs7137665	0.81[CHB][hapmap];0.81[CHD][hapmap];0.84[ASN][1000 genomes]
rs7137809	0.86[JPT][hapmap]
rs721709	0.81[CHB][hapmap];0.84[CHD][hapmap];0.84[ASN][1000 genomes]
rs721711	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs721712	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs721713	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7298930	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7302503	0.81[CHB][hapmap];0.84[CHD][hapmap];0.84[ASN][1000 genomes]
rs7302841	0.88[YRI][hapmap];0.87[AFR][1000 genomes]
rs7305344	0.81[CHB][hapmap]
rs7307276	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7308560	0.86[JPT][hapmap]
rs7310390	0.81[JPT][hapmap]
rs7957057	0.84[CHD][hapmap]
rs7972535	0.86[JPT][hapmap]
rs7973058	0.90[CHB][hapmap]
rs7973479	0.84[CHB][hapmap]
rs7975124	0.81[JPT][hapmap]
rs963243	0.85[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs994798	0.86[JPT][hapmap]

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	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv832377	chr12:40704881-40855223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7307562	FXYD2	trans	lymphoblastoid	seeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
2	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
3	chr12:40656800-40746400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:40674400-40760400	Weak transcription	Lung	lung
5	chr12:40681200-40763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:40684000-40725000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:40687200-40765000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:40712000-40736600	Weak transcription	Left Ventricle	heart
9	chr12:40712000-40743400	Weak transcription	Aorta	Aorta
10	chr12:40714200-40759200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:40716800-40761600	Weak transcription	Fetal Kidney	kidney
12	chr12:40719600-40735200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:40721000-40734000	Weak transcription	Esophagus	oesophagus
14	chr12:40721600-40726000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr12:40722400-40725600	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:40722400-40726200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:40722400-40730800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:40722400-40736200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:40722600-40725200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:40722600-40728600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:40722600-40730200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:40722800-40725000	Weak transcription	Ovary	ovary
23	chr12:40722800-40755800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:40723200-40725600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:40723600-40725000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
26	chr12:40723800-40725200	ZNF genes & repeats	Adipose Nuclei	Adipose
27	chr12:40723800-40725400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
28	chr12:40723800-40725600	ZNF genes & repeats	A549	lung
29	chr12:40724000-40731600	Weak transcription	Brain Angular Gyrus	brain
30	chr12:40724200-40729600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:40724200-40731400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:40724400-40725200	ZNF genes & repeats	Primary B cells from cord blood	blood
33	chr12:40724600-40725000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
34	chr12:40724600-40725200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:40724600-40745400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr12:40724800-40725200	ZNF genes & repeats	Liver	Liver
37	chr12:40724800-40728600	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:40724800-40729600	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr12:40724800-40751000	Weak transcription	Brain Anterior Caudate	brain

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