Variant report

Variant	rs1864393
Chromosome Location	chr10:43658653-43658654
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43649271..43651758-chr10:43657631..43659326,2	K562	blood:
2	chr10:43657144..43659807-chr10:43661487..43664434,2	MCF-7	breast:
3	chr10:43631805..43635298-chr10:43656697..43658657,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169826	Chromatin interaction
ENSG00000273008	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10159558	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238441	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11238465	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12258585	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12260994	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12262152	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12765436	0.93[ASN][1000 genomes]
rs12765715	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12765838	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12766298	0.93[ASN][1000 genomes]
rs12773930	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12775330	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12775743	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12779732	0.93[ASN][1000 genomes]
rs12783340	1.00[CHB][hapmap]
rs17158594	0.82[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap]
rs17363630	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799939	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1800863	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1879298	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs1879299	0.82[AMR][1000 genomes]
rs2075911	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28401552	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2900627	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3026776	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3026779	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3026781	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3026782	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34817887	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4987091	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7067798	0.82[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs7074319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086299	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71505665	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71505667	0.93[ASN][1000 genomes]
rs71505668	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72783237	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72783242	0.93[ASN][1000 genomes]
rs7893332	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7903283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910648	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921281	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7923256	1.00[CEU][hapmap];0.88[AMR][1000 genomes]
rs9804209	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[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	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1042310	chr10:43623060-43688505	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1864393	TMEM72	cis	cerebellum	SCAN
rs1864393	ZNF22	cis	parietal	SCAN
rs1864393	RET	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43635600-43689000	Weak transcription	Esophagus	oesophagus
2	chr10:43647200-43667800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:43647400-43667800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr10:43647600-43659600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr10:43647600-43664000	Weak transcription	Fetal Brain Male	brain
6	chr10:43647600-43667000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr10:43649200-43661600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr10:43650400-43667600	Weak transcription	Brain Germinal Matrix	brain
9	chr10:43651000-43671800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr10:43652400-43668600	Weak transcription	Fetal Heart	heart
11	chr10:43652600-43667800	Weak transcription	Brain Substantia Nigra	brain
12	chr10:43652600-43669800	Weak transcription	Right Ventricle	heart
13	chr10:43652600-43697200	Weak transcription	Pancreas	Pancrea
14	chr10:43653000-43668000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr10:43653200-43663800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:43653400-43667400	Weak transcription	Fetal Intestine Small	intestine
17	chr10:43654600-43678000	Weak transcription	Hela-S3	cervix
18	chr10:43655000-43680600	Weak transcription	Colonic Mucosa	Colon
19	chr10:43655400-43660400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr10:43655400-43663000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:43655600-43659000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr10:43655600-43659400	Strong transcription	Dnd41	blood
23	chr10:43655800-43659800	Strong transcription	Primary T cells from cord blood	blood
24	chr10:43655800-43673000	Weak transcription	Fetal Kidney	kidney
25	chr10:43656000-43659400	Strong transcription	Fetal Brain Female	brain
26	chr10:43656000-43660600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr10:43656000-43667200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr10:43656000-43667400	Weak transcription	Brain Hippocampus Middle	brain
29	chr10:43656000-43674800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr10:43656200-43660000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr10:43656200-43660000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr10:43656200-43660200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr10:43656400-43659000	Strong transcription	Fetal Intestine Large	intestine
34	chr10:43656400-43659400	Strong transcription	Fetal Muscle Leg	muscle
35	chr10:43656400-43660000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr10:43656400-43660000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr10:43656400-43660000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr10:43656400-43660000	Strong transcription	Fetal Muscle Trunk	muscle
39	chr10:43656400-43664200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr10:43656400-43673400	Weak transcription	Psoas Muscle	Psoas
41	chr10:43656600-43660000	Strong transcription	Fetal Stomach	stomach
42	chr10:43656600-43660200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr10:43656600-43660600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr10:43656800-43659200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr10:43656800-43659400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr10:43656800-43660200	Strong transcription	Ovary	ovary
47	chr10:43656800-43660400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr10:43657000-43658800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr10:43657000-43659000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr10:43657000-43659000	Strong transcription	Aorta	Aorta

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