Variant report

Variant	rs1888945
Chromosome Location	chr9:97822567-97822568
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97822176..97825096-chr9:97827855..97830416,5	MCF-7	breast:
2	chr9:97626134..97628785-chr9:97822106..97824115,2	K562	blood:
3	chr9:97815564..97817505-chr9:97820080..97822608,2	MCF-7	breast:
4	chr9:97821527..97823304-chr9:97837475..97839849,2	MCF-7	breast:
5	chr9:97821556..97825075-chr9:97832512..97834984,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1020962	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1038092	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761371	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993471	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553869	0.96[ASN][1000 genomes]
rs12555829	1.00[ASN][1000 genomes]
rs1564235	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571896	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699499	0.86[EUR][1000 genomes]
rs1871220	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888944	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888946	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061798	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061799	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2061801	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306207	1.00[ASN][1000 genomes]
rs3739748	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780560	0.80[ASN][1000 genomes]
rs4743975	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743977	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743978	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743989	0.80[ASN][1000 genomes]
rs4744421	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744429	1.00[ASN][1000 genomes]
rs4744437	0.93[ASN][1000 genomes]
rs4744440	0.86[ASN][1000 genomes]
rs6479596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67134693	0.96[ASN][1000 genomes]
rs7039768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046900	0.93[ASN][1000 genomes]
rs72750335	0.96[ASN][1000 genomes]
rs72750346	0.96[ASN][1000 genomes]
rs72750351	0.96[ASN][1000 genomes]
rs72750359	0.96[ASN][1000 genomes]
rs72750367	1.00[ASN][1000 genomes]
rs72750373	1.00[ASN][1000 genomes]
rs73540087	1.00[ASN][1000 genomes]
rs9299427	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97813400-97827200	Genic enhancers	Liver	Liver
3	chr9:97815200-97824400	Weak transcription	Thymus	Thymus
4	chr9:97816000-97823000	Enhancers	Fetal Heart	heart
5	chr9:97817600-97826000	Genic enhancers	HepG2	liver
6	chr9:97817600-97826400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:97818000-97822800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:97818000-97824400	Weak transcription	GM12878-XiMat	blood
9	chr9:97818200-97823000	Enhancers	Stomach Mucosa	stomach
10	chr9:97818400-97825000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:97818800-97830400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr9:97819000-97824600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:97819200-97823400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:97819200-97824200	Weak transcription	Adipose Nuclei	Adipose
15	chr9:97819200-97824400	Weak transcription	HUVEC	blood vessel
16	chr9:97819600-97824200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:97819800-97822600	Enhancers	Fetal Muscle Leg	muscle
18	chr9:97819800-97822800	Enhancers	NH-A	brain
19	chr9:97819800-97823200	Enhancers	Brain Angular Gyrus	brain
20	chr9:97819800-97824200	Weak transcription	HMEC	breast
21	chr9:97819800-97826000	Genic enhancers	HSMM	muscle
22	chr9:97820000-97822800	Enhancers	Brain Cingulate Gyrus	brain
23	chr9:97820000-97822800	Weak transcription	Small Intestine	intestine
24	chr9:97820000-97823000	Enhancers	Fetal Lung	lung
25	chr9:97820000-97824600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:97820000-97854200	Weak transcription	Fetal Brain Male	brain
27	chr9:97820200-97823000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr9:97820200-97825000	Enhancers	Brain Substantia Nigra	brain
29	chr9:97820400-97822800	Weak transcription	Fetal Intestine Large	intestine
30	chr9:97820400-97825600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:97820400-97840800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:97820400-97843000	Weak transcription	Primary T cells from cord blood	blood
33	chr9:97820600-97824200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr9:97820600-97824800	Weak transcription	Fetal Kidney	kidney
35	chr9:97820600-97825600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr9:97820800-97823000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:97820800-97823000	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr9:97820800-97823200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:97820800-97823400	Genic enhancers	Fetal Stomach	stomach
41	chr9:97821000-97824200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:97821000-97838400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr9:97821200-97822800	Enhancers	NHLF	lung
44	chr9:97821200-97823600	Enhancers	Brain Hippocampus Middle	brain
45	chr9:97821200-97823600	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr9:97821200-97823600	Genic enhancers	Right Ventricle	heart
47	chr9:97821200-97824200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr9:97821200-97824600	Weak transcription	Spleen	Spleen
49	chr9:97821200-97839000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:97821200-97839600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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