Variant report

Variant	rs11900089
Chromosome Location	chr2:113004097-113004098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113002423..113004405-chr2:113031977..113033609,2	MCF-7	breast:
2	chr2:113001621..113004129-chr2:113004849..113007814,3	MCF-7	breast:
3	chr2:113002216..113004918-chr2:113009956..113011920,4	K562	blood:
4	chr2:112994848..112996456-chr2:113003331..113004834,2	MCF-7	breast:
5	chr2:112999545..113001797-chr2:113002175..113005170,3	K562	blood:
6	chr2:113003810..113005815-chr2:113009554..113011676,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144161	Chromatin interaction
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11898975	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11900153	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465398	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12614282	0.96[ASN][1000 genomes]
rs12622246	0.96[ASN][1000 genomes]
rs12623743	0.87[ASN][1000 genomes]
rs13001618	0.90[ASN][1000 genomes]
rs2254860	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2312459	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35502956	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv3422414	chr2:112883450-113200285	Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv582703	chr2:112920219-113100014	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv874867	chr2:112930064-113038409	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv1805614	chr2:112949713-113048705	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11900089	RGPD8	cis	Artery Tibial	GTEx
rs11900089	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs11900089	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs11900089	RGPD8	cis	lung	GTEx
rs11900089	RGPD8	cis	Nerve Tibial	GTEx
rs11900089	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs11900089	RGPD8	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112961000-113009000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:112968000-113011800	Weak transcription	Right Ventricle	heart
3	chr2:112968200-113009200	Weak transcription	Small Intestine	intestine
4	chr2:112968200-113012000	Weak transcription	Pancreas	Pancrea
5	chr2:112968800-113011400	Weak transcription	Brain Angular Gyrus	brain
6	chr2:112968800-113011800	Weak transcription	Brain Substantia Nigra	brain
7	chr2:112969000-113005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:112969400-113011800	Weak transcription	Esophagus	oesophagus
9	chr2:112969600-113009000	Weak transcription	Psoas Muscle	Psoas
10	chr2:112970200-113004800	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:112970800-113005200	Weak transcription	Gastric	stomach
12	chr2:112970800-113011600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:112971400-113011600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:112971800-113011800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:112978200-113006400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:112979000-113004400	Weak transcription	Lung	lung
17	chr2:112979600-113011600	Weak transcription	Fetal Kidney	kidney
18	chr2:112979600-113012000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:112980000-113004600	Weak transcription	Placenta	Placenta
20	chr2:112980000-113005400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:112980000-113011800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:112980200-113011600	Weak transcription	HSMM	muscle
23	chr2:112987200-113010800	Weak transcription	NH-A	brain
24	chr2:112987200-113011000	Weak transcription	NHDF-Ad	bronchial
25	chr2:112987400-113005600	Weak transcription	Aorta	Aorta
26	chr2:112987400-113011400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:112987800-113011000	Weak transcription	NHEK	skin
28	chr2:112987800-113011800	Weak transcription	NHLF	lung
29	chr2:112988400-113011600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:112990800-113009200	Weak transcription	Hela-S3	cervix
31	chr2:112992200-113011400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:112992200-113011800	Weak transcription	HSMMtube	muscle
33	chr2:112993000-113011000	Weak transcription	HMEC	breast
34	chr2:112993400-113011000	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:112994600-113008800	Weak transcription	Spleen	Spleen
36	chr2:112994600-113011800	Weak transcription	Colonic Mucosa	Colon
37	chr2:112994800-113004400	Weak transcription	Fetal Stomach	stomach
38	chr2:112994800-113005200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:112995400-113005400	Weak transcription	Fetal Intestine Small	intestine
40	chr2:112997600-113007000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr2:112998800-113004800	Strong transcription	Primary B cells from cord blood	blood
42	chr2:112998800-113005800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:112999000-113006800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:112999200-113007000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr2:112999200-113007600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr2:112999800-113008800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:113000600-113008400	Strong transcription	Fetal Thymus	thymus
48	chr2:113000800-113007600	Weak transcription	K562	blood
49	chr2:113000800-113009400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:113000800-113009600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links