Variant report

Variant	rs2277184
Chromosome Location	chr9:98239147-98239148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98238631..98241380-chr9:98256472..98259143,2	K562	blood:
2	chr9:98228127..98229820-chr9:98239088..98240889,2	K562	blood:
3	chr9:98236732..98239700-chr9:98240483..98242788,2	MCF-7	breast:
4	chr9:98238893..98240402-chr9:98242216..98244216,2	K562	blood:
5	chr9:98233432..98236653-chr9:98236835..98241063,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271314	Chromatin interaction
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs16905572	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2236405	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2274690	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2277183	0.90[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28413575	0.94[ASN][1000 genomes]
rs28735184	0.93[ASN][1000 genomes]
rs3824487	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57305472	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	nsv1051665	chr9:98234404-98264577	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2277184	CHAD	trans	brain	seeQTL
rs2277184	ANO8	trans	brain	seeQTL
rs2277184	KCNJ16	trans	brain	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
2	chr9:98225800-98239600	Weak transcription	HMEC	breast
3	chr9:98225800-98239800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:98225800-98244000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:98226000-98248400	Weak transcription	HUVEC	blood vessel
6	chr9:98226000-98251000	Weak transcription	Osteobl	bone
7	chr9:98226200-98239400	Weak transcription	NHEK	skin
8	chr9:98226200-98240800	Strong transcription	Fetal Intestine Large	intestine
9	chr9:98226200-98243400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:98226200-98254000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:98226400-98239200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr9:98226400-98239400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:98226400-98243000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:98226400-98247800	Weak transcription	Stomach Mucosa	stomach
15	chr9:98226600-98239200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:98226600-98239400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr9:98226600-98239600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr9:98226600-98239600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr9:98226600-98240000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr9:98226600-98240200	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr9:98226600-98253800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr9:98226800-98239400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:98227000-98242600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:98227000-98242800	Strong transcription	Fetal Muscle Leg	muscle
25	chr9:98227000-98243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:98227000-98243600	Strong transcription	Fetal Intestine Small	intestine
27	chr9:98227200-98239200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr9:98227200-98243000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr9:98227200-98243000	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr9:98227200-98244800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:98227400-98239600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:98227400-98242000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:98227400-98242800	Strong transcription	Adipose Nuclei	Adipose
34	chr9:98227600-98248800	Weak transcription	Small Intestine	intestine
35	chr9:98227800-98243200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr9:98228000-98240400	Strong transcription	Left Ventricle	heart
37	chr9:98228000-98243400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:98228600-98239200	Strong transcription	Brain Hippocampus Middle	brain
39	chr9:98229800-98246800	Weak transcription	Colon Smooth Muscle	Colon
40	chr9:98231000-98239800	Weak transcription	HSMM	muscle
41	chr9:98231400-98239400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:98231400-98239400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr9:98231600-98239400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:98231600-98239400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:98231800-98240200	Weak transcription	Fetal Heart	heart
46	chr9:98231800-98240800	Weak transcription	A549	lung
47	chr9:98232200-98241200	Weak transcription	K562	blood
48	chr9:98232200-98261200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr9:98233200-98240800	Weak transcription	NHDF-Ad	bronchial
50	chr9:98233400-98242800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links