Variant report

Variant	rs11015592
Chromosome Location	chr10:18969276-18969277
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:18938885..18940645-chr10:18967631..18969812,2	K562	blood:
2	chr10:18962456..18966517-chr10:18966877..18973376,6	K562	blood:
3	chr10:18966816..18969348-chr10:18971030..18973085,3	K562	blood:
4	chr10:18969086..18970965-chr10:18973281..18975325,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CACNB2-1	chr10:18967049-18970567	NONHSAT011652

Variant related genes	Relation type
ENSG00000241058	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10828973	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11014582	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11014594	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11014660	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11014696	1.00[AMR][1000 genomes]
rs11014721	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11014733	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11014797	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11014800	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11014805	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11014825	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11014831	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11014961	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11014985	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11014990	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015001	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015020	0.86[EUR][1000 genomes]
rs11015022	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015033	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015034	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015046	0.86[EUR][1000 genomes]
rs11015060	0.86[EUR][1000 genomes]
rs11015065	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015066	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015089	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11015091	0.91[EUR][1000 genomes]
rs11015100	0.91[EUR][1000 genomes]
rs11015104	0.91[EUR][1000 genomes]
rs11015180	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11015185	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11015366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11015514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11015519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11015533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11015540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11492557	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11511205	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11516859	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12355664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12355670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12356125	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12356280	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12356286	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12356533	0.80[EUR][1000 genomes]
rs12357063	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12357123	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12357491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12358173	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12360352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17620201	0.89[AMR][1000 genomes]
rs17622004	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17622211	0.91[EUR][1000 genomes]
rs17622520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4279920	0.91[EUR][1000 genomes]
rs4497294	0.86[EUR][1000 genomes]
rs45452100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4570480	1.00[AMR][1000 genomes];0.86[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	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18949400-18973200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:18949600-18972000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:18951000-18971800	Weak transcription	Spleen	Spleen
4	chr10:18951000-18976400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:18951400-18973800	Weak transcription	Aorta	Aorta
6	chr10:18954400-18973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:18955000-18972600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:18956000-18970000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:18956000-18972200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr10:18956200-18973200	Weak transcription	Small Intestine	intestine
11	chr10:18957400-18971600	Weak transcription	Fetal Heart	heart
12	chr10:18957600-18969600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr10:18957600-18971200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr10:18957800-18971000	Weak transcription	Brain Anterior Caudate	brain
15	chr10:18958200-18969800	Weak transcription	NHEK	skin
16	chr10:18958200-18970000	Weak transcription	HSMMtube	muscle
17	chr10:18959000-18973600	Weak transcription	Left Ventricle	heart
18	chr10:18960000-18972400	Weak transcription	Brain Hippocampus Middle	brain
19	chr10:18960200-18969800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr10:18960400-18970200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr10:18960800-18970200	Weak transcription	NHLF	lung
22	chr10:18960800-18973400	Weak transcription	Ovary	ovary
23	chr10:18961000-18970800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr10:18961000-18973600	Weak transcription	Thymus	Thymus
25	chr10:18961600-18971000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:18961800-18970200	Weak transcription	HMEC	breast
27	chr10:18962400-18973600	Weak transcription	Fetal Intestine Small	intestine
28	chr10:18962400-18973600	Weak transcription	Fetal Stomach	stomach
29	chr10:18963200-18973400	Weak transcription	Pancreas	Pancrea
30	chr10:18963800-18970000	Weak transcription	NHDF-Ad	bronchial
31	chr10:18964000-18972200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr10:18964000-18973000	Weak transcription	Primary T cells from cord blood	blood
33	chr10:18964200-18973400	Weak transcription	Psoas Muscle	Psoas
34	chr10:18964600-18973600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr10:18964600-18973800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr10:18964800-18969800	Weak transcription	Osteobl	bone
37	chr10:18964800-18970000	Weak transcription	A549	lung
38	chr10:18964800-18970400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr10:18964800-18970800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr10:18964800-18973400	Weak transcription	Fetal Brain Female	brain
41	chr10:18964800-18973400	Weak transcription	HUVEC	blood vessel
42	chr10:18964800-18973800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr10:18965000-18972800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr10:18965000-18973400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr10:18965200-18970000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr10:18965200-18971600	Weak transcription	Placenta	Placenta
47	chr10:18965200-18972200	Weak transcription	Fetal Muscle Leg	muscle
48	chr10:18965200-18972400	Weak transcription	Colon Smooth Muscle	Colon
49	chr10:18965200-18973400	Weak transcription	Brain Germinal Matrix	brain
50	chr10:18965200-18973400	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links