Variant report

Variant	rs12083800
Chromosome Location	chr1:9856826-9856827
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9855972..9858555-chr1:9861978..9863923,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11121482	1.00[MEX][hapmap]
rs12059243	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12068953	1.00[MEX][hapmap]
rs12072320	0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12084163	0.87[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12087408	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12092457	0.93[ASW][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12094930	0.87[AMR][1000 genomes]
rs12096905	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12354258	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12354385	0.89[AFR][1000 genomes]
rs6658971	0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6663532	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7514164	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9887930	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv2298	chr1:9826286-9857487	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv827586	chr1:9846555-9857371	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv1819093	chr1:9847032-9856826	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1824318	chr1:9847032-9856826	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv1845506	chr1:9847032-9856826	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv1847729	chr1:9847032-9856826	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv1822763	chr1:9847032-9864493	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9811800-9857000	Weak transcription	Aorta	Aorta
2	chr1:9843000-9864400	Weak transcription	Stomach Mucosa	stomach
3	chr1:9843400-9858400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:9845800-9858200	Weak transcription	HMEC	breast
5	chr1:9847200-9858200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:9847400-9859800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:9848200-9857200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:9848200-9857200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:9848200-9860000	Weak transcription	Primary B cells from cord blood	blood
10	chr1:9848400-9857200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr1:9848400-9858600	Weak transcription	Primary T cells from cord blood	blood
12	chr1:9848600-9857200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:9848600-9864600	Weak transcription	Small Intestine	intestine
14	chr1:9849200-9858400	Weak transcription	Adipose Nuclei	Adipose
15	chr1:9852000-9857000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:9852600-9859000	Weak transcription	Placenta	Placenta
17	chr1:9852800-9857000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:9852800-9857000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:9852800-9857200	Weak transcription	Fetal Stomach	stomach
20	chr1:9852800-9857800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:9852800-9858200	Weak transcription	Fetal Lung	lung
22	chr1:9853000-9857000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:9853000-9858400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:9853000-9858400	Weak transcription	Hela-S3	cervix
25	chr1:9853000-9858400	Weak transcription	HSMMtube	muscle
26	chr1:9853000-9858800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:9853200-9857000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:9853600-9857000	Weak transcription	Spleen	Spleen
29	chr1:9854000-9857000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:9854000-9858200	Weak transcription	NHEK	skin
31	chr1:9854000-9858800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:9854000-9864600	Weak transcription	Fetal Intestine Small	intestine
33	chr1:9854000-9871600	Weak transcription	Brain Germinal Matrix	brain
34	chr1:9854200-9857800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:9854200-9858200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:9854200-9858400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:9854200-9858400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr1:9854200-9858400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:9854200-9859800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:9854200-9865200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:9854400-9857200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:9854400-9858600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr1:9854400-9865200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:9854600-9857000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:9854600-9857000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:9854600-9857000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:9854600-9857000	Weak transcription	Fetal Thymus	thymus
48	chr1:9854600-9857000	Weak transcription	Ovary	ovary
49	chr1:9854600-9857200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:9854600-9857200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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