Variant report

Variant	rs12341506
Chromosome Location	chr9:136740971-136740972
allele	A/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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136695295..136698632-chr9:136737582..136741114,3	MCF-7	breast:
2	chr9:136738620..136740987-chr9:136829938..136833023,3	MCF-7	breast:
3	chr2:238395363..238396972-chr9:136738845..136741262,2	MCF-7	breast:
4	chr9:136644385..136647944-chr9:136738272..136741517,4	MCF-7	breast:
5	chr9:136733619..136743972-chr9:136852076..136861381,50	MCF-7	breast:
6	chr9:136698753..136701712-chr9:136736999..136741089,4	MCF-7	breast:
7	chr9:136736947..136741233-chr9:136835339..136839101,5	MCF-7	breast:
8	chr9:136737400..136743457-chr9:136819359..136829756,12	MCF-7	breast:
9	chr9:136736139..136748779-chr9:136853521..136861128,82	MCF-7	breast:
10	chr9:136701985..136719064-chr9:136732605..136742545,35	MCF-7	breast:
11	chr9:136738615..136741064-chr9:136782245..136785156,2	MCF-7	breast:
12	chr9:136723768..136727391-chr9:136738428..136742111,4	MCF-7	breast:
13	chr9:136738092..136740992-chr9:136890169..136892007,2	MCF-7	breast:
14	chr9:136707781..136709506-chr9:136739982..136742386,2	MCF-7	breast:
15	chr9:136685827..136689292-chr9:136739053..136741402,3	MCF-7	breast:
16	chr9:136703509..136705855-chr9:136737754..136741325,4	MCF-7	breast:
17	chr9:136737792..136741016-chr9:136774631..136778412,3	MCF-7	breast:
18	chr9:136658148..136661518-chr9:136735926..136740986,7	MCF-7	breast:
19	chr9:136739328..136742123-chr9:136841796..136845434,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction
ENSG00000235106	Chromatin interaction
ENSG00000115648	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10116143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10116617	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10993825	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10993831	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10993837	1.00[JPT][hapmap]
rs11507039	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12001190	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12115818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12336628	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347121	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2510250	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs3763660	1.00[CEU][hapmap]
rs3780740	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780783	1.00[CEU][hapmap]
rs73559892	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869522	1.00[JPT][hapmap]

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:66 , 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	chr9:136735600-136744200	Weak transcription	Fetal Brain Male	brain
4	chr9:136735600-136747400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:136735800-136741400	Weak transcription	Gastric	stomach
6	chr9:136735800-136742400	Weak transcription	GM12878-XiMat	blood
7	chr9:136736000-136760000	Weak transcription	Primary B cells from cord blood	blood
8	chr9:136736400-136745200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr9:136736800-136756200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:136737000-136743000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:136737200-136742800	Enhancers	Fetal Muscle Leg	muscle
12	chr9:136737200-136749000	Enhancers	Placenta Amnion	Placenta Amnion
13	chr9:136738200-136743000	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr9:136738400-136741000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:136738400-136741000	Enhancers	Fetal Stomach	stomach
16	chr9:136738400-136741400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:136738400-136741400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:136738400-136741800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr9:136738400-136742000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:136738400-136742400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:136738400-136742600	Enhancers	Esophagus	oesophagus
22	chr9:136738400-136743800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:136738400-136744800	Genic enhancers	Fetal Intestine Small	intestine
24	chr9:136738800-136741200	Weak transcription	Brain Substantia Nigra	brain
25	chr9:136738800-136742000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr9:136738800-136744400	Weak transcription	Fetal Brain Female	brain
27	chr9:136738800-136746000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr9:136738800-136746400	Weak transcription	Right Atrium	heart
29	chr9:136739000-136741400	Enhancers	HSMMtube	muscle
30	chr9:136739200-136741800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr9:136739200-136742400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:136739400-136741800	Weak transcription	Brain Hippocampus Middle	brain
33	chr9:136739400-136744400	Enhancers	Pancreas	Pancrea
34	chr9:136739400-136746400	Weak transcription	Fetal Lung	lung
35	chr9:136739600-136742000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr9:136739800-136741800	Enhancers	HepG2	liver
37	chr9:136739800-136742600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:136739800-136747600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr9:136739800-136748000	Enhancers	Liver	Liver
40	chr9:136739800-136748200	Weak transcription	Fetal Thymus	thymus
41	chr9:136740000-136741400	Enhancers	HSMM	muscle
42	chr9:136740000-136741800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:136740000-136741800	Enhancers	A549	lung
44	chr9:136740000-136743200	Enhancers	HMEC	breast
45	chr9:136740000-136747200	Weak transcription	NHLF	lung
46	chr9:136740000-136754800	Weak transcription	Osteobl	bone
47	chr9:136740200-136741000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr9:136740200-136741200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:136740200-136747000	Weak transcription	Lung	lung
50	chr9:136740200-136757400	Weak transcription	Duodenum Mucosa	Duodenum

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