Variant report

Variant	rs12344469
Chromosome Location	chr9:94708676-94708677
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:94667534..94670775-chr9:94707582..94710553,5	K562	blood:
2	chr9:94706737..94709425-chr9:94709648..94712474,2	MCF-7	breast:
3	chr9:94646595..94649139-chr9:94708273..94710120,2	K562	blood:
4	chr9:94706769..94709242-chr9:94710784..94712955,2	MCF-7	breast:
5	chr9:94533336..94534896-chr9:94707634..94709527,2	MCF-7	breast:
6	chr9:94708402..94710475-chr9:94715730..94717686,2	K562	blood:
7	chr9:94661900..94664292-chr9:94705248..94709269,4	K562	blood:

Variant related genes	Relation type
ENSG00000169071	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10046835	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10114686	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10115262	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10118409	0.81[AFR][1000 genomes]
rs10118781	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10120655	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121928	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10122619	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10124705	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10124796	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10992160	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10992163	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10992175	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12340061	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12349001	0.81[EUR][1000 genomes]
rs12349258	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1919104	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28477960	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs56266486	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs57496363	0.81[EUR][1000 genomes]
rs57862149	0.81[EUR][1000 genomes]
rs58964193	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59195968	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59917975	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60351369	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61266489	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7027147	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7033888	0.81[EUR][1000 genomes]
rs7035117	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7036958	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7043019	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7045073	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7045603	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73519176	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73520858	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73520881	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73520889	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73522907	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs73522929	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7851412	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7856148	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7863425	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7867659	0.83[AFR][1000 genomes];0.81[EUR][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	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv530946	chr9:94633154-94715023	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv831653	chr9:94692454-94867542	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv982625	chr9:94702344-94712887	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94706200-94710400	Enhancers	Placenta Amnion	Placenta Amnion
2	chr9:94706400-94708800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr9:94706800-94709600	Flanking Active TSS	K562	blood
4	chr9:94707000-94708800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:94707000-94708800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:94707000-94709800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr9:94707200-94708800	Enhancers	Placenta	Placenta
8	chr9:94707400-94708800	Enhancers	Colonic Mucosa	Colon
9	chr9:94707400-94710400	Weak transcription	Gastric	stomach
10	chr9:94707600-94708800	Flanking Active TSS	Hela-S3	cervix
11	chr9:94707600-94709000	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr9:94707600-94709400	Bivalent Enhancer	Fetal Intestine Large	intestine
13	chr9:94707600-94709600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:94707600-94709800	Enhancers	Fetal Intestine Small	intestine
15	chr9:94707600-94710400	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr9:94707800-94709200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:94708000-94709000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr9:94708000-94709200	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:94708000-94709400	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr9:94708200-94708800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:94708200-94709000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr9:94708200-94709200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:94708200-94709200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:94708200-94709600	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr9:94708200-94710400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr9:94708400-94708800	Active TSS	Fetal Kidney	kidney
27	chr9:94708400-94708800	Enhancers	NHLF	lung
28	chr9:94708400-94709000	Flanking Active TSS	Rectal Smooth Muscle	rectum
29	chr9:94708400-94709200	Enhancers	Ovary	ovary
30	chr9:94708400-94709200	Enhancers	Right Atrium	heart
31	chr9:94708400-94709200	Bivalent Enhancer	Stomach Mucosa	stomach
32	chr9:94708400-94709400	Enhancers	Fetal Heart	heart
33	chr9:94708400-94710000	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr9:94708400-94710400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:94708600-94708800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
36	chr9:94708600-94708800	Bivalent Enhancer	Esophagus	oesophagus
37	chr9:94708600-94708800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr9:94708600-94708800	Bivalent Enhancer	Fetal Thymus	thymus
39	chr9:94708600-94709000	Enhancers	Fetal Lung	lung
40	chr9:94708600-94709600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:94708600-94710200	Enhancers	Fetal Stomach	stomach
42	chr9:94708600-94710400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr9:94708600-94710600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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