Variant report

Variant	rs10749920
Chromosome Location	chr11:108383676-108383677
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:108368444..108370288-chr11:108381123..108383752,3	K562	blood:
2	chr11:108366425..108370806-chr11:108379844..108383752,5	K562	blood:

Variant related genes	Relation type
ENSG00000178202	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10789666	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890851	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10890852	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890853	0.84[CEU][hapmap];0.92[CHB][hapmap];0.81[EUR][1000 genomes]
rs10890855	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10890858	0.84[CEU][hapmap]
rs10890859	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11212682	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11212689	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11212691	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11212695	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11212700	0.84[CEU][hapmap];0.92[CHB][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11212704	0.92[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs11824250	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12362341	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17092330	0.82[CEU][hapmap]
rs1940219	0.84[CEU][hapmap]
rs2016291	0.91[EUR][1000 genomes]
rs2846412	0.88[LWK][hapmap];0.88[YRI][hapmap]
rs3741060	0.92[CEU][hapmap];0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs3900699	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4442514	0.84[CEU][hapmap]
rs4533001	0.84[CEU][hapmap]
rs4643041	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4753844	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4754325	0.83[ASN][1000 genomes]
rs4754326	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7104503	0.92[CEU][hapmap];0.92[CHB][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7118229	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10749920	KDELC2	cis	multi-tissue	Pritchard
rs10749920	KDELC2	Cis_1M	lymphoblastoid	RTeQTL
rs10749920	ACAT1	cis	cerebellum	SCAN
rs10749920	KDELC2	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108369600-108384000	Weak transcription	Fetal Kidney	kidney
2	chr11:108370400-108408800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:108371800-108406400	Weak transcription	Gastric	stomach
4	chr11:108372000-108401200	Weak transcription	Esophagus	oesophagus
5	chr11:108377600-108384400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:108379800-108389200	Strong transcription	Placenta	Placenta
7	chr11:108380000-108384200	Genic enhancers	NHEK	skin
8	chr11:108380200-108384800	Weak transcription	Brain Anterior Caudate	brain
9	chr11:108380400-108384400	Weak transcription	Stomach Mucosa	stomach
10	chr11:108380800-108384000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:108380800-108384000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:108380800-108384000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:108381000-108385600	Strong transcription	Liver	Liver
14	chr11:108381000-108408800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr11:108381600-108383800	Enhancers	HMEC	breast
16	chr11:108381600-108385400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:108381800-108384200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:108382000-108384000	Weak transcription	GM12878-XiMat	blood
19	chr11:108382000-108384200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr11:108382000-108384200	Weak transcription	Primary T cells from cord blood	blood
21	chr11:108382000-108384400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr11:108382000-108384400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr11:108382000-108396000	Weak transcription	Pancreas	Pancrea
24	chr11:108382200-108384000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr11:108382200-108384400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:108382200-108385000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr11:108382200-108385600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:108382200-108385600	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr11:108382600-108385600	Strong transcription	K562	blood
30	chr11:108382800-108383800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr11:108382800-108384000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:108383000-108384200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr11:108383000-108384800	Weak transcription	Brain Substantia Nigra	brain
34	chr11:108383000-108385400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:108383000-108385600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr11:108383000-108398400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr11:108383200-108384000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr11:108383400-108384400	Weak transcription	HSMM	muscle
39	chr11:108383400-108385400	Strong transcription	Lung	lung
40	chr11:108383400-108385600	Strong transcription	Aorta	Aorta
41	chr11:108383400-108386600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr11:108383400-108387000	Weak transcription	Left Ventricle	heart
43	chr11:108383600-108383800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:108383600-108384000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr11:108383600-108385600	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr11:108383600-108385600	Strong transcription	HSMMtube	muscle
47	chr11:108383600-108386400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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