Variant report

Variant	rs12341869
Chromosome Location	chr9:108054503-108054504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr9:108054256-108054617	T-47D	breast:	n/a	n/a
2	TEAD4	chr9:108053853-108054603	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:108048778..108051200-chr9:108054042..108056380,2	MCF-7	breast:
2	chr9:108052363..108054677-chr9:108071523..108074219,3	MCF-7	breast:
3	chr9:108005087..108008498-chr9:108050324..108055404,7	MCF-7	breast:
4	chr9:108053038..108054954-chr9:108056839..108058571,2	K562	blood:
5	chr9:108052475..108054719-chr9:108057760..108060481,3	MCF-7	breast:
6	chr9:108051884..108054784-chr9:108055791..108058847,3	MCF-7	breast:
7	chr9:108007303..108009573-chr9:108053805..108056055,2	MCF-7	breast:
8	chr9:108053113..108055212-chr9:108060978..108062866,2	MCF-7	breast:

No data

Variant related genes	Relation type
SLC44A1	TF binding region
ENSG00000070214	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs28688962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57877883	1.00[AMR][1000 genomes]
rs59290851	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6479300	0.90[AFR][1000 genomes]
rs6479301	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479302	0.84[ASW][hapmap];0.83[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479303	0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479304	0.84[ASW][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7024012	0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7026389	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7031663	0.82[MKK][hapmap]
rs7033929	0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7039638	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7046185	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7048497	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72744219	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72744225	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73510211	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510218	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510246	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510280	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510281	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510289	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510295	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666622	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666624	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666625	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7847744	0.82[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7847952	0.84[AFR][1000 genomes]
rs7853038	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7853709	0.83[AMR][1000 genomes]
rs7854064	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7854282	1.00[AMR][1000 genomes]
rs7857088	0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7860356	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7869261	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7873924	0.90[YRI][hapmap];0.83[AMR][1000 genomes]
rs7874307	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9777083	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893685	chr9:107940737-108083485	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv893686	chr9:107968330-108083485	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893687	chr9:107973277-108083485	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv893688	chr9:107974761-108083485	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv893690	chr9:107992706-108083485	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108033200-108056200	Weak transcription	Primary T cells from cord blood	blood
2	chr9:108043600-108057400	Weak transcription	HSMM	muscle
3	chr9:108043600-108059400	Weak transcription	NHLF	lung
4	chr9:108043600-108059800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:108044800-108056600	Weak transcription	Hela-S3	cervix
6	chr9:108049400-108074200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:108049800-108057400	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr9:108050200-108054800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:108050200-108061400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr9:108050200-108061800	Weak transcription	Fetal Stomach	stomach
11	chr9:108050600-108056000	Enhancers	Placenta	Placenta
12	chr9:108051000-108057800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr9:108051000-108061600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:108051200-108055000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr9:108051400-108056600	Enhancers	Brain Hippocampus Middle	brain
16	chr9:108052400-108054600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:108052400-108054600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr9:108052400-108054600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr9:108052400-108056600	Enhancers	Brain Angular Gyrus	brain
20	chr9:108052400-108061400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:108052600-108055400	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr9:108052600-108058200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr9:108052600-108058200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr9:108052800-108054800	Enhancers	Liver	Liver
25	chr9:108052800-108054800	Enhancers	Fetal Lung	lung
26	chr9:108052800-108055200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr9:108052800-108055800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr9:108052800-108056400	Enhancers	Brain Cingulate Gyrus	brain
29	chr9:108052800-108056600	Enhancers	Brain Anterior Caudate	brain
30	chr9:108052800-108058000	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr9:108052800-108061400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:108053000-108054600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:108053000-108056000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:108053000-108056000	Enhancers	Fetal Heart	heart
35	chr9:108053000-108063000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr9:108053200-108054600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:108053200-108054600	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr9:108053200-108057600	Weak transcription	Small Intestine	intestine
39	chr9:108053200-108058400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:108053400-108055000	Enhancers	Colon Smooth Muscle	Colon
41	chr9:108053400-108056600	Weak transcription	Osteobl	bone
42	chr9:108053400-108061400	Weak transcription	Aorta	Aorta
43	chr9:108053600-108055200	Enhancers	Ovary	ovary
44	chr9:108053600-108055600	Weak transcription	Brain Germinal Matrix	brain
45	chr9:108053600-108058600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr9:108053600-108060000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr9:108053600-108061600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:108053800-108054600	Enhancers	Psoas Muscle	Psoas
49	chr9:108053800-108057800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:108053800-108059800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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