Variant report

Variant	rs2846412
Chromosome Location	chr11:108384207-108384208
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDELC2-1	chr11:108384134-108385602	NONHSAT024036

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10431062	0.80[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10749920	0.88[LWK][hapmap];0.88[YRI][hapmap]
rs10789666	0.95[LWK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs10890851	0.83[AFR][1000 genomes]
rs10890852	0.81[YRI][hapmap]
rs11212691	0.82[AFR][1000 genomes]
rs12361570	0.82[JPT][hapmap]
rs4753844	0.88[YRI][hapmap]
rs7104503	0.82[YRI][hapmap]
rs7943820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv832263	chr11:108183372-108384391	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2846412	KDELC2	Cis_1M	lymphoblastoid	RTeQTL
rs2846412	GRIA4	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108370400-108408800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:108371800-108406400	Weak transcription	Gastric	stomach
3	chr11:108372000-108401200	Weak transcription	Esophagus	oesophagus
4	chr11:108377600-108384400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:108379800-108389200	Strong transcription	Placenta	Placenta
6	chr11:108380200-108384800	Weak transcription	Brain Anterior Caudate	brain
7	chr11:108380400-108384400	Weak transcription	Stomach Mucosa	stomach
8	chr11:108381000-108385600	Strong transcription	Liver	Liver
9	chr11:108381000-108408800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr11:108381600-108385400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:108382000-108384400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:108382000-108384400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr11:108382000-108396000	Weak transcription	Pancreas	Pancrea
14	chr11:108382200-108384400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:108382200-108385000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr11:108382200-108385600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr11:108382200-108385600	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr11:108382600-108385600	Strong transcription	K562	blood
19	chr11:108383000-108384800	Weak transcription	Brain Substantia Nigra	brain
20	chr11:108383000-108385400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:108383000-108385600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr11:108383000-108398400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:108383400-108384400	Weak transcription	HSMM	muscle
24	chr11:108383400-108385400	Strong transcription	Lung	lung
25	chr11:108383400-108385600	Strong transcription	Aorta	Aorta
26	chr11:108383400-108386600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr11:108383400-108387000	Weak transcription	Left Ventricle	heart
28	chr11:108383600-108385600	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr11:108383600-108385600	Strong transcription	HSMMtube	muscle
30	chr11:108383600-108386400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr11:108383800-108384600	Weak transcription	HMEC	breast
32	chr11:108383800-108385000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:108383800-108385400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:108383800-108386200	Weak transcription	Colonic Mucosa	Colon
35	chr11:108384000-108384800	Strong transcription	GM12878-XiMat	blood
36	chr11:108384000-108385000	Strong transcription	Fetal Kidney	kidney
37	chr11:108384000-108385200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
38	chr11:108384000-108385400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr11:108384000-108385600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr11:108384000-108385600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:108384000-108385600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr11:108384000-108390600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:108384200-108385000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr11:108384200-108385200	Strong transcription	Primary T cells from cord blood	blood
45	chr11:108384200-108385400	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr11:108384200-108385600	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr11:108384200-108387600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:108384200-108389200	Strong transcription	NHEK	skin

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