Variant report

Variant	rs12001216
Chromosome Location	chr9:136745965-136745966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136656812..136664739-chr9:136743672..136748217,7	MCF-7	breast:
2	chr9:136736139..136748779-chr9:136853521..136861128,82	MCF-7	breast:
3	chr9:136745470..136748380-chr9:136799363..136801099,3	MCF-7	breast:
4	chr9:136712521..136714249-chr9:136744359..136747348,2	MCF-7	breast:
5	chr9:136695961..136698474-chr9:136744886..136747596,2	MCF-7	breast:
6	chr9:136744004..136756386-chr9:136850728..136860313,29	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10739995	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10821533	0.84[CEU][hapmap]
rs10993826	0.83[CEU][hapmap]
rs10993836	0.83[CEU][hapmap]
rs10993837	1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10993842	0.84[CEU][hapmap]
rs12001180	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12002290	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12002767	0.84[CEU][hapmap]
rs2073929	0.83[CEU][hapmap]
rs3780737	0.91[CEU][hapmap]
rs3780739	0.84[CEU][hapmap]
rs3780741	0.91[CEU][hapmap]
rs3819500	0.83[CEU][hapmap]
rs3819502	0.83[CEU][hapmap]
rs7025939	0.82[CEU][hapmap]
rs7038256	0.82[CEU][hapmap]
rs7852459	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7853626	0.83[CEU][hapmap]
rs7869522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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:68 , 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	chr9:136738800-136746000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr9:136738800-136746400	Weak transcription	Right Atrium	heart
9	chr9:136739400-136746400	Weak transcription	Fetal Lung	lung
10	chr9:136739800-136747600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:136739800-136748000	Enhancers	Liver	Liver
12	chr9:136739800-136748200	Weak transcription	Fetal Thymus	thymus
13	chr9:136740000-136747200	Weak transcription	NHLF	lung
14	chr9:136740000-136754800	Weak transcription	Osteobl	bone
15	chr9:136740200-136747000	Weak transcription	Lung	lung
16	chr9:136740200-136757400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr9:136740400-136746400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:136740400-136746400	Weak transcription	Spleen	Spleen
19	chr9:136741400-136746000	Weak transcription	HSMMtube	muscle
20	chr9:136741400-136746600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:136741400-136747200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr9:136741800-136746200	Weak transcription	NH-A	brain
23	chr9:136741800-136746400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr9:136741800-136747000	Weak transcription	Gastric	stomach
25	chr9:136741800-136753000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr9:136741800-136753200	Weak transcription	A549	lung
27	chr9:136742000-136747400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr9:136742000-136747400	Weak transcription	Brain Substantia Nigra	brain
29	chr9:136742400-136747400	Weak transcription	Brain Hippocampus Middle	brain
30	chr9:136743000-136746400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:136744000-136755200	Enhancers	Fetal Muscle Leg	muscle
32	chr9:136744400-136746000	Enhancers	Fetal Muscle Trunk	muscle
33	chr9:136744400-136748400	Enhancers	Fetal Brain Female	brain
34	chr9:136744400-136751200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr9:136744600-136748000	Genic enhancers	Fetal Stomach	stomach
36	chr9:136744600-136748600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr9:136744600-136751600	Weak transcription	Fetal Intestine Large	intestine
38	chr9:136744600-136751800	Weak transcription	GM12878-XiMat	blood
39	chr9:136744600-136753000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr9:136744800-136746200	Strong transcription	Fetal Intestine Small	intestine
41	chr9:136744800-136747400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:136745000-136746200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr9:136745000-136746200	Weak transcription	Fetal Brain Male	brain
44	chr9:136745200-136746200	Enhancers	Primary B cells from peripheral blood	blood
45	chr9:136745200-136747000	Genic enhancers	HepG2	liver
46	chr9:136745200-136747000	Enhancers	HMEC	breast
47	chr9:136745200-136747400	Enhancers	Pancreas	Pancrea
48	chr9:136745200-136747600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr9:136745400-136746000	Genic enhancers	NHEK	skin
50	chr9:136745400-136746200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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