Variant report

Variant	rs10843814
Chromosome Location	chr12:30846055-30846056
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:30840570..30842757-chr12:30843253..30846337,3	K562	blood:
2	chr12:30845389..30848478-chr12:30907681..30910609,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSPAN11-10	chr12:30845902-30846912	ucscGeneNc_uc001rjo_1

Variant related genes	Relation type
ENSG00000133704	Chromatin interaction
ENSG00000110888	Chromatin interaction
ENSG00000246331	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10444423	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734793	0.85[ASN][1000 genomes]
rs10743729	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10771745	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10771756	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771757	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771760	0.86[ASN][1000 genomes]
rs10771761	0.86[ASN][1000 genomes]
rs10771762	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10771768	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10843804	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10843813	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843815	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843817	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843818	0.86[ASN][1000 genomes]
rs10843819	0.86[ASN][1000 genomes]
rs10843820	0.86[ASN][1000 genomes]
rs10843821	0.86[ASN][1000 genomes]
rs10843822	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10843823	0.86[ASN][1000 genomes]
rs10843824	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10843827	0.85[ASN][1000 genomes]
rs10843828	0.85[ASN][1000 genomes]
rs10843829	0.83[ASN][1000 genomes]
rs10843831	0.84[ASN][1000 genomes]
rs10843832	0.85[ASN][1000 genomes]
rs10843833	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs10843834	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10843835	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11051005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051008	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051010	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11051027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051045	0.86[ASN][1000 genomes]
rs11051047	0.85[ASN][1000 genomes]
rs11051048	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051049	0.85[ASN][1000 genomes]
rs11051050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11051053	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11051061	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11051063	0.81[ASN][1000 genomes]
rs11835180	0.85[ASN][1000 genomes]
rs12146709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12303852	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12368923	0.86[ASN][1000 genomes]
rs12369125	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12370947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12579616	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12809335	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12825440	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12826615	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12830910	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241828	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278558	0.86[EUR][1000 genomes]
rs2289302	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304630	0.90[JPT][hapmap]
rs35133495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35336533	0.86[ASN][1000 genomes]
rs36074842	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4082413	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4335626	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59177896	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61923728	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487928	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487934	0.86[ASN][1000 genomes]
rs6487936	0.86[ASN][1000 genomes]
rs6487939	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7299800	0.86[ASN][1000 genomes]
rs7304221	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7952744	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7955804	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7957141	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7958274	0.83[ASN][1000 genomes]
rs7958276	0.85[ASN][1000 genomes]
rs7966063	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971762	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7971870	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7979718	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980510	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][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	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10843814	IPO8	cis	multi-tissue	Pritchard
rs10843814	IPO8	Cis_1M	lymphoblastoid	RTeQTL
rs10843814	IPO8	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30780800-30847000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:30785000-30847800	Weak transcription	Gastric	stomach
3	chr12:30785200-30846400	Weak transcription	Spleen	Spleen
4	chr12:30785400-30847200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:30821800-30847200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:30821800-30847400	Weak transcription	Lung	lung
7	chr12:30822000-30846600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:30822600-30846400	Weak transcription	Esophagus	oesophagus
9	chr12:30822600-30847400	Weak transcription	Aorta	Aorta
10	chr12:30827000-30847000	Weak transcription	Colonic Mucosa	Colon
11	chr12:30830400-30846600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:30831800-30846400	Weak transcription	Thymus	Thymus
13	chr12:30831800-30846600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:30831800-30846800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:30832200-30846800	Weak transcription	Fetal Stomach	stomach
16	chr12:30833600-30846600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:30833600-30847000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:30834800-30846400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr12:30834800-30847000	Weak transcription	Stomach Mucosa	stomach
20	chr12:30836600-30846400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:30837400-30846400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr12:30837400-30847000	Weak transcription	Fetal Thymus	thymus
23	chr12:30837600-30846400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:30837600-30846600	Weak transcription	Fetal Kidney	kidney
25	chr12:30837600-30847000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:30838200-30846400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:30838400-30847400	Weak transcription	Placenta	Placenta
28	chr12:30838600-30847400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:30838800-30846200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:30839600-30846400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr12:30839600-30846400	Weak transcription	Fetal Intestine Large	intestine
32	chr12:30839600-30846600	Weak transcription	Fetal Intestine Small	intestine
33	chr12:30839600-30846800	Weak transcription	Fetal Muscle Leg	muscle
34	chr12:30839600-30847000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:30840800-30847000	Weak transcription	Primary B cells from cord blood	blood
36	chr12:30843200-30846800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:30844000-30847000	Enhancers	NHEK	skin
38	chr12:30844200-30846800	Enhancers	Hela-S3	cervix
39	chr12:30844200-30847400	Enhancers	HUVEC	blood vessel
40	chr12:30844400-30846600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr12:30844400-30846800	Enhancers	HepG2	liver
42	chr12:30844600-30846400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:30844600-30846400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:30844600-30846400	Weak transcription	K562	blood
45	chr12:30844600-30846600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr12:30844600-30846600	Weak transcription	Fetal Heart	heart
47	chr12:30844600-30846600	Weak transcription	HMEC	breast
48	chr12:30844600-30846800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:30844600-30846800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:30844600-30846800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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