Variant report

Variant	rs10041551
Chromosome Location	chr5:94046205-94046206
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIAA0825-2	chr5:94044217-94046398	NONHSAT102832

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10035632	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10035650	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs10037228	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10039801	1.00[CHB][hapmap]
rs10041262	0.87[ASN][1000 genomes]
rs10041843	0.87[ASN][1000 genomes]
rs10043779	1.00[CHB][hapmap]
rs10044797	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051931	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053484	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10056685	0.91[CEU][hapmap]
rs10058130	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10058618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059194	1.00[CHB][hapmap]
rs10061737	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062248	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070258	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs10076188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10076461	0.87[ASN][1000 genomes]
rs10078049	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078304	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10476612	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs10476613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10476615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949227	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11953346	0.82[ASW][hapmap]
rs11955373	0.96[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960129	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516225	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs12517866	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs12518034	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs12522312	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13169956	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13353994	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13354061	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13358642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13361811	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13362556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17083818	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs28645132	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28787271	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs293032	1.00[ASW][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap]
rs306573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs306575	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869218	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55974730	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6862592	0.87[ASN][1000 genomes]
rs6873364	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs755898	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7705424	0.95[CEU][hapmap]
rs7725095	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725698	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731360	0.89[EUR][1000 genomes]
rs7737779	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9314118	0.82[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	nsv462254	chr5:93956937-94056825	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv598953	chr5:93956937-94056825	ZNF genes & repeats Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv882387	chr5:94001476-94071404	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10041551	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs10041551	C5orf36	cis	cerebellum	SCAN
rs10041551	TIMM22	trans	lymphoblastoid	seeQTL
rs10041551	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs10041551	ANKRD32	cis	multi-tissue	Pritchard

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93991200-94049000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:93994200-94047200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr5:93994400-94048800	Weak transcription	Small Intestine	intestine
4	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
5	chr5:93996600-94048400	Weak transcription	Lung	lung
6	chr5:94012600-94048400	Weak transcription	Aorta	Aorta
7	chr5:94012600-94048400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:94012600-94049000	Weak transcription	Left Ventricle	heart
9	chr5:94012600-94051000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:94012600-94053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:94020200-94048400	Weak transcription	Psoas Muscle	Psoas
12	chr5:94020800-94050000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:94023200-94046400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:94023200-94049800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:94023200-94050400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:94023200-94051000	Weak transcription	Thymus	Thymus
17	chr5:94023400-94050400	Weak transcription	Fetal Muscle Leg	muscle
18	chr5:94023400-94051800	Weak transcription	Fetal Intestine Small	intestine
19	chr5:94024600-94046600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr5:94024600-94051800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:94025800-94050800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:94025800-94050800	Weak transcription	K562	blood
23	chr5:94025800-94051400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:94026400-94051600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:94028000-94050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:94028000-94051600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:94029000-94051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:94029200-94049000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:94029200-94050400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr5:94029200-94051800	Weak transcription	Brain Germinal Matrix	brain
31	chr5:94029200-94052400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:94029400-94048800	Weak transcription	HMEC	breast
33	chr5:94029400-94051200	Weak transcription	Fetal Brain Male	brain
34	chr5:94029400-94051400	Weak transcription	Fetal Heart	heart
35	chr5:94029800-94050000	Weak transcription	Osteobl	bone
36	chr5:94030200-94051400	Weak transcription	HSMM	muscle
37	chr5:94031000-94047400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:94031000-94050000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr5:94031000-94050000	Weak transcription	Liver	Liver
40	chr5:94031000-94051200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr5:94031000-94052000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:94031200-94046800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr5:94031200-94050600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:94034200-94051400	Weak transcription	Pancreas	Pancrea
45	chr5:94035400-94052000	Weak transcription	Fetal Kidney	kidney
46	chr5:94037400-94051000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr5:94039000-94050800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr5:94039000-94064600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:94039800-94052000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr5:94040200-94050600	Strong transcription	Monocytes-CD14+_RO01746	blood

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