Variant report

Variant	rs7852459
Chromosome Location	chr9:136747239-136747240
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136746436..136748479-chr9:136750005..136751914,2	K562	blood:
2	chr9:136747018..136748827-chr9:136855326..136857970,2	K562	blood:
3	chr9:136656812..136664739-chr9:136743672..136748217,7	MCF-7	breast:
4	chr9:136747201..136749377-chr9:136761194..136763291,2	MCF-7	breast:
5	chr9:136747124..136749714-chr9:136809806..136812182,3	MCF-7	breast:
6	chr9:136736139..136748779-chr9:136853521..136861128,82	MCF-7	breast:
7	chr9:136745470..136748380-chr9:136799363..136801099,3	MCF-7	breast:
8	chr9:136747009..136748873-chr9:136778099..136780165,2	MCF-7	breast:
9	chr9:136712521..136714249-chr9:136744359..136747348,2	MCF-7	breast:
10	chr9:136662777..136665043-chr9:136746286..136748398,2	MCF-7	breast:
11	chr9:136695961..136698474-chr9:136744886..136747596,2	MCF-7	breast:
12	chr9:136746415..136748463-chr9:136851208..136853267,2	MCF-7	breast:
13	chr9:136744004..136756386-chr9:136850728..136860313,29	MCF-7	breast:
14	chr9:136746155..136749193-chr9:136766163..136768175,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10739995	0.86[EUR][1000 genomes]
rs10821528	0.83[EUR][1000 genomes]
rs10821533	0.83[CEU][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10993836	0.87[CEU][hapmap]
rs10993839	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10993842	0.83[CEU][hapmap];0.88[ASN][1000 genomes]
rs12001180	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs12001216	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12002290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12002767	0.83[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2073830	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs2156323	1.00[MEX][hapmap]
rs3780737	0.82[EUR][1000 genomes]
rs3780739	0.87[CEU][hapmap]
rs3780741	0.87[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs3858104	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61034217	0.83[EUR][1000 genomes]
rs7021948	0.81[EUR][1000 genomes]
rs7025939	1.00[CHB][hapmap]
rs7038256	1.00[CHB][hapmap]
rs7869522	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9657700	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	nsv894114	chr9:136538798-136779153	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv831745	chr9:136593702-136780273	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv831746	chr9:136607829-136750740	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv894122	chr9:136632662-136760639	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1035272	chr9:136665308-136772256	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv894123	chr9:136682408-136852501	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv894124	chr9:136716399-136870787	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv894125	chr9:136723520-136931957	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136729600-136780000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr9:136729800-136762600	Weak transcription	Right Ventricle	heart
3	chr9:136735600-136747400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:136736000-136760000	Weak transcription	Primary B cells from cord blood	blood
5	chr9:136736800-136756200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:136737200-136749000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr9:136739800-136747600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:136739800-136748000	Enhancers	Liver	Liver
9	chr9:136739800-136748200	Weak transcription	Fetal Thymus	thymus
10	chr9:136740000-136754800	Weak transcription	Osteobl	bone
11	chr9:136740200-136757400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr9:136741800-136753000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr9:136741800-136753200	Weak transcription	A549	lung
14	chr9:136742000-136747400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr9:136742000-136747400	Weak transcription	Brain Substantia Nigra	brain
16	chr9:136742400-136747400	Weak transcription	Brain Hippocampus Middle	brain
17	chr9:136744000-136755200	Enhancers	Fetal Muscle Leg	muscle
18	chr9:136744400-136748400	Enhancers	Fetal Brain Female	brain
19	chr9:136744400-136751200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr9:136744600-136748000	Genic enhancers	Fetal Stomach	stomach
21	chr9:136744600-136748600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr9:136744600-136751600	Weak transcription	Fetal Intestine Large	intestine
23	chr9:136744600-136751800	Weak transcription	GM12878-XiMat	blood
24	chr9:136744600-136753000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr9:136744800-136747400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:136745200-136747400	Enhancers	Pancreas	Pancrea
27	chr9:136745200-136747600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:136745400-136747600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:136745400-136748200	Enhancers	Placenta	Placenta
30	chr9:136745400-136748600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr9:136745400-136749600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:136745600-136748200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr9:136745600-136748800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:136745600-136749000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:136745600-136749600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:136745600-136754600	Weak transcription	Hela-S3	cervix
37	chr9:136745800-136747800	Enhancers	Brain Germinal Matrix	brain
38	chr9:136745800-136748800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:136745800-136748800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:136745800-136748800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr9:136745800-136748800	Enhancers	Esophagus	oesophagus
42	chr9:136745800-136755600	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr9:136746000-136747400	Weak transcription	Brain Anterior Caudate	brain
44	chr9:136746000-136747600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr9:136746000-136747600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
46	chr9:136746000-136748600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr9:136746000-136748800	Enhancers	HSMMtube	muscle
48	chr9:136746200-136747800	Enhancers	NH-A	brain
49	chr9:136746200-136748200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:136746200-136748600	Genic enhancers	Fetal Intestine Small	intestine

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