Variant report

Variant	rs12338907
Chromosome Location	chr9:97952231-97952232
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97906541..97908120-chr9:97951638..97953781,2	MCF-7	breast:
2	chr9:97950616..97952464-chr9:98272435..98274822,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10283758	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10993475	0.87[EUR][1000 genomes]
rs10993479	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10993483	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10993503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10993520	0.81[AMR][1000 genomes]
rs1105979	0.83[AMR][1000 genomes]
rs12337959	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12339700	0.83[AMR][1000 genomes]
rs12342782	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344626	0.82[EUR][1000 genomes]
rs12350646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377946	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17679141	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs1886992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1889241	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs28626189	0.84[EUR][1000 genomes]
rs28658564	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4237226	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647372	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647373	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647401	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647404	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647432	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647441	1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4743990	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4744443	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs4744444	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4744445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744453	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4744458	0.81[AMR][1000 genomes]
rs56134407	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62560523	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7357617	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs879559	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97930800-97952400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:97941000-97959800	Weak transcription	Pancreas	Pancrea
3	chr9:97945600-97952400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:97945800-97952800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:97946200-97955600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:97946200-97955800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:97948400-97952400	Weak transcription	HMEC	breast
8	chr9:97948800-97955600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:97948800-97955600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:97950200-97952400	Enhancers	K562	blood
11	chr9:97950400-97952400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr9:97950400-97952400	Enhancers	Brain Substantia Nigra	brain
13	chr9:97950400-97952600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:97950400-97952600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr9:97950400-97952600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr9:97950400-97953000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:97950600-97952400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:97950600-97952400	Flanking Active TSS	HUVEC	blood vessel
19	chr9:97950600-97952600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr9:97950600-97952600	Enhancers	Fetal Intestine Small	intestine
21	chr9:97950600-97952800	Enhancers	Primary T cells from cord blood	blood
22	chr9:97950600-97953400	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr9:97950800-97952400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr9:97950800-97952400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr9:97950800-97952600	Enhancers	Fetal Muscle Leg	muscle
26	chr9:97950800-97952800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr9:97950800-97959600	Weak transcription	Gastric	stomach
28	chr9:97951000-97952400	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr9:97951000-97952400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:97951000-97952600	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr9:97951000-97952800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:97951200-97952400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:97951200-97952600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr9:97951200-97952600	Enhancers	Fetal Kidney	kidney
35	chr9:97951400-97952600	Enhancers	Brain Anterior Caudate	brain
36	chr9:97951400-97952800	Enhancers	Brain Germinal Matrix	brain
37	chr9:97951400-97953000	Enhancers	Right Ventricle	heart
38	chr9:97951600-97952400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr9:97951600-97952400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr9:97951600-97952400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:97951600-97952400	Enhancers	Liver	Liver
42	chr9:97951600-97952400	Enhancers	GM12878-XiMat	blood
43	chr9:97951600-97952400	Enhancers	HSMMtube	muscle
44	chr9:97951600-97952800	Enhancers	Colon Smooth Muscle	Colon
45	chr9:97951600-97953200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr9:97951800-97952400	Enhancers	Adipose Nuclei	Adipose
47	chr9:97951800-97952400	Enhancers	Stomach Mucosa	stomach
48	chr9:97951800-97952600	Enhancers	Fetal Thymus	thymus
49	chr9:97951800-97953000	Enhancers	Right Atrium	heart
50	chr9:97951800-97953000	Enhancers	Skeletal Muscle Female	skeletal muscle

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