Variant report

Variant	rs28601668
Chromosome Location	chr9:98245716-98245717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98243853..98250190-chr9:98264163..98273969,14	MCF-7	breast:
2	chr9:98239525..98243679-chr9:98243925..98247581,3	K562	blood:
3	chr9:98241516..98243611-chr9:98244641..98247119,2	K562	blood:

Variant related genes	Relation type
ENSG00000185920	Chromatin interaction
ENSG00000271155	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16909898	1.00[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs16909902	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs16909938	1.00[CEU][hapmap]
rs2275104	1.00[CEU][hapmap]
rs2282040	1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs28390100	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28429270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28441412	0.84[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.80[MKK][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28446116	0.89[LWK][hapmap];0.83[MKK][hapmap]
rs28448271	0.94[AFR][1000 genomes]
rs28474857	0.92[AFR][1000 genomes]
rs28535536	0.84[LWK][hapmap]
rs28673156	0.92[AFR][1000 genomes]
rs28676757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28698995	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4647396	1.00[CEU][hapmap]
rs4647399	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	nsv824994	chr9:98239963-98314431	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv824995	chr9:98243455-98326547	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv824996	chr9:98245375-98283861	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 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	chr9:98226000-98248400	Weak transcription	HUVEC	blood vessel
3	chr9:98226000-98251000	Weak transcription	Osteobl	bone
4	chr9:98226200-98254000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr9:98226400-98247800	Weak transcription	Stomach Mucosa	stomach
6	chr9:98226600-98253800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr9:98227600-98248800	Weak transcription	Small Intestine	intestine
8	chr9:98229800-98246800	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:98232200-98261200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:98238200-98246400	Weak transcription	Psoas Muscle	Psoas
11	chr9:98239400-98247200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:98239400-98251400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:98239600-98253800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr9:98239800-98260000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:98240000-98247600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:98240400-98246400	Weak transcription	Right Ventricle	heart
18	chr9:98240400-98256200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:98240800-98259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:98241000-98258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:98241200-98248800	Weak transcription	Colonic Mucosa	Colon
22	chr9:98241600-98246400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:98242000-98245800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:98242000-98251200	Weak transcription	K562	blood
25	chr9:98242000-98256400	Weak transcription	Esophagus	oesophagus
26	chr9:98242200-98256200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr9:98242400-98245800	Weak transcription	Gastric	stomach
28	chr9:98242400-98246400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr9:98242400-98246400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:98242400-98253400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr9:98242400-98253600	Weak transcription	Spleen	Spleen
32	chr9:98242400-98256200	Weak transcription	NHLF	lung
33	chr9:98242400-98266400	Weak transcription	HSMMtube	muscle
34	chr9:98242600-98245800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr9:98242600-98246000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr9:98242600-98246400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr9:98242600-98247800	Weak transcription	Liver	Liver
38	chr9:98242600-98256200	Weak transcription	Placenta	Placenta
39	chr9:98242800-98245800	Weak transcription	Left Ventricle	heart
40	chr9:98242800-98245800	Weak transcription	Lung	lung
41	chr9:98242800-98246000	Weak transcription	Fetal Heart	heart
42	chr9:98242800-98246400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:98242800-98246400	Weak transcription	Pancreas	Pancrea
44	chr9:98242800-98246800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr9:98242800-98253800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr9:98242800-98256600	Weak transcription	Fetal Kidney	kidney
47	chr9:98242800-98266600	Weak transcription	Adipose Nuclei	Adipose
48	chr9:98243000-98245800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:98243000-98246400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr9:98243000-98246400	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links