Variant report

Variant	rs4979349
Chromosome Location	chr9:116942415-116942416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116940947..116942974-chr9:116968939..116970805,2	MCF-7	breast:
2	chr9:116938315..116939926-chr9:116941668..116944207,2	MCF-7	breast:
3	chr9:116940464..116942565-chr9:116943951..116946533,3	K562	blood:
4	chr9:116927426..116928989-chr9:116941833..116943417,2	K562	blood:
5	chr9:116932183..116936074-chr9:116938591..116942808,3	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10739404	0.87[EUR][1000 genomes]
rs10739405	0.88[EUR][1000 genomes]
rs10739406	0.96[ASN][1000 genomes]
rs10759683	0.85[EUR][1000 genomes]
rs10759684	0.91[EUR][1000 genomes]
rs10759688	0.96[ASN][1000 genomes]
rs10817576	0.89[EUR][1000 genomes]
rs10982092	0.86[EUR][1000 genomes]
rs12343445	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1431819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2060132	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2567704	0.96[ASN][1000 genomes]
rs4406486	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4978568	0.90[EUR][1000 genomes]
rs4978571	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4979345	0.90[EUR][1000 genomes]
rs4979346	0.92[EUR][1000 genomes]
rs4979347	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979351	0.96[ASN][1000 genomes]
rs7855790	0.90[EUR][1000 genomes]
rs7870521	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
4	esv2761285	chr9:116811897-117103268	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
5	nsv870215	chr9:116842614-117070344	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	124 gene(s)	inside rSNPs	diseases
6	nsv893752	chr9:116899258-116944333	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv466532	chr9:116930100-116957958	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv615232	chr9:116930100-116957958	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv466533	chr9:116930100-117248479	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS 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	128 gene(s)	inside rSNPs	diseases
10	nsv615233	chr9:116930100-117248479	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	128 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116919200-116972000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:116926200-116943800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:116926400-116950200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:116926400-116950400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr9:116930600-116954400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:116931000-116946400	Genic enhancers	Fetal Stomach	stomach
7	chr9:116931000-116971800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:116932800-116943800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:116932800-116971800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr9:116934400-116942800	Enhancers	Colon Smooth Muscle	Colon
11	chr9:116935000-116946600	Enhancers	Liver	Liver
12	chr9:116935200-116944800	Enhancers	Fetal Heart	heart
13	chr9:116935200-116944800	Enhancers	Left Ventricle	heart
14	chr9:116935200-116945400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr9:116936400-116944400	Enhancers	Placenta	Placenta
16	chr9:116937600-116943000	Weak transcription	Colonic Mucosa	Colon
17	chr9:116937600-116943000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr9:116937600-116943000	Weak transcription	Stomach Mucosa	stomach
19	chr9:116937800-116943000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:116937800-116943400	Weak transcription	Brain Substantia Nigra	brain
21	chr9:116938000-116942800	Weak transcription	Fetal Thymus	thymus
22	chr9:116938000-116943200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:116938000-116956200	Weak transcription	Gastric	stomach
24	chr9:116938600-116944000	Enhancers	Right Ventricle	heart
25	chr9:116938800-116943600	Weak transcription	Brain Anterior Caudate	brain
26	chr9:116939000-116944200	Enhancers	Right Atrium	heart
27	chr9:116939200-116948800	Weak transcription	Brain Germinal Matrix	brain
28	chr9:116939400-116967200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:116939600-116943200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr9:116939800-116943200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr9:116940000-116942800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr9:116940000-116943800	Weak transcription	Fetal Kidney	kidney
33	chr9:116940200-116943800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:116940200-116950000	Genic enhancers	Fetal Muscle Leg	muscle
35	chr9:116940400-116942800	Genic enhancers	Fetal Muscle Trunk	muscle
36	chr9:116940400-116946200	Weak transcription	Hela-S3	cervix
37	chr9:116940400-116965200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr9:116940600-116942600	Strong transcription	Fetal Intestine Large	intestine
39	chr9:116940600-116942600	Strong transcription	Fetal Intestine Small	intestine
40	chr9:116940600-116942600	Strong transcription	HepG2	liver
41	chr9:116940600-116943000	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:116940600-116943200	Weak transcription	HUVEC	blood vessel
43	chr9:116940600-116943400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr9:116940600-116946800	Weak transcription	A549	lung
45	chr9:116940600-116947800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr9:116940600-116955800	Weak transcription	HMEC	breast
47	chr9:116940800-116942800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr9:116940800-116943200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr9:116940800-116945600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:116941000-116943400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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