Variant report

Variant	rs16909877
Chromosome Location	chr9:98216645-98216646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98209521..98214013-chr9:98214744..98218073,4	K562	blood:
2	chr9:98077820..98081322-chr9:98214829..98218712,4	K562	blood:
3	chr9:98195732..98198631-chr9:98215123..98217873,2	K562	blood:
4	chr9:98210280..98213178-chr9:98213473..98216650,4	K562	blood:
5	chr9:98187259..98193172-chr9:98208629..98217669,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237857	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12685109	1.00[AMR][1000 genomes]
rs16905568	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16912143	1.00[AMR][1000 genomes]
rs173339	1.00[JPT][hapmap]
rs2227970	0.93[ASN][1000 genomes]
rs2765817	1.00[JPT][hapmap]
rs28522014	1.00[AMR][1000 genomes]
rs356663	1.00[JPT][hapmap]
rs356671	1.00[JPT][hapmap]
rs55758638	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55787302	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56222079	1.00[AMR][1000 genomes]
rs651009	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv949520	chr9:98204199-98238358	Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1053762	chr9:98208542-98232120	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16909877	AKR1C2	trans	brain	seeQTL
rs16909877	ALDH1A2	trans	brain	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98202000-98224600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:98204400-98220400	Strong transcription	Fetal Intestine Large	intestine
3	chr9:98204800-98224400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:98205200-98218000	Weak transcription	Small Intestine	intestine
5	chr9:98206000-98224400	Weak transcription	HUVEC	blood vessel
6	chr9:98206000-98237600	Weak transcription	Psoas Muscle	Psoas
7	chr9:98206200-98221400	Strong transcription	Fetal Intestine Small	intestine
8	chr9:98206400-98217600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr9:98206400-98218400	Weak transcription	NHEK	skin
10	chr9:98206600-98217200	Strong transcription	Liver	Liver
11	chr9:98206600-98220200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:98206600-98220200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:98206600-98220400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr9:98206600-98221200	Strong transcription	Brain Hippocampus Middle	brain
15	chr9:98206600-98223000	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:98206600-98224000	Strong transcription	Adipose Nuclei	Adipose
17	chr9:98206600-98224600	Strong transcription	Aorta	Aorta
18	chr9:98206600-98225200	Strong transcription	Pancreas	Pancrea
19	chr9:98206800-98219200	Strong transcription	Gastric	stomach
20	chr9:98207000-98221000	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr9:98207000-98221800	Strong transcription	Ovary	ovary
22	chr9:98207000-98223000	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr9:98207200-98219400	Strong transcription	Brain Substantia Nigra	brain
24	chr9:98207200-98223200	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr9:98207200-98224400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr9:98207400-98224200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr9:98207600-98224400	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr9:98208000-98224400	Weak transcription	HSMM	muscle
29	chr9:98208400-98220000	Weak transcription	NH-A	brain
30	chr9:98208600-98224000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:98209200-98219000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:98209200-98220200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr9:98209400-98218200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:98209400-98222600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr9:98209600-98218000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr9:98209600-98224000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr9:98209600-98224400	Weak transcription	NHDF-Ad	bronchial
38	chr9:98209800-98217000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:98209800-98219800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr9:98210000-98218400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr9:98210400-98223800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr9:98210600-98221800	Strong transcription	Brain Cingulate Gyrus	brain
43	chr9:98210800-98221200	Strong transcription	Fetal Muscle Leg	muscle
44	chr9:98210800-98221800	Strong transcription	Fetal Muscle Trunk	muscle
45	chr9:98211200-98224200	Strong transcription	Left Ventricle	heart
46	chr9:98211400-98224600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr9:98211600-98218200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:98211800-98218200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr9:98211800-98222600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:98212000-98224600	Strong transcription	Skeletal Muscle Female	skeletal muscle

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