Variant report

Variant	rs12096905
Chromosome Location	chr1:9874158-9874159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9872577..9875298-chr1:9882585..9884745,2	MCF-7	breast:
2	chr1:9867658..9869307-chr1:9873212..9875276,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12059243	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12072320	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12083800	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12084163	0.87[AMR][1000 genomes]
rs12087408	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12092457	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12094930	0.87[AMR][1000 genomes]
rs12354258	0.87[AMR][1000 genomes]
rs12354385	0.84[AFR][1000 genomes]
rs6658971	0.87[AMR][1000 genomes]
rs6663532	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7514164	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9887930	0.85[AFR][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	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	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

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9859000-9875000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr1:9859000-9881800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:9859000-9882400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:9859200-9874200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:9859200-9874800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr1:9859400-9881600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:9860400-9878600	Weak transcription	Primary B cells from cord blood	blood
8	chr1:9865000-9874600	Weak transcription	Fetal Intestine Large	intestine
9	chr1:9865000-9874800	Weak transcription	Placenta	Placenta
10	chr1:9865000-9882200	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:9865400-9881600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:9865600-9877000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:9865600-9879000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:9865600-9880800	Weak transcription	Hela-S3	cervix
15	chr1:9865600-9882200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:9866400-9880600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:9868200-9874800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:9868200-9874800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:9868200-9875000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:9868200-9882600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:9868400-9880800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:9868400-9880800	Weak transcription	Primary T cells from cord blood	blood
23	chr1:9868400-9882600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:9869200-9874800	Weak transcription	Colonic Mucosa	Colon
25	chr1:9869200-9880800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:9869200-9882600	Weak transcription	Esophagus	oesophagus
27	chr1:9869400-9874600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:9869400-9882600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:9869600-9877000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:9869600-9877000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:9869600-9877000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:9869600-9880200	Weak transcription	Dnd41	blood
33	chr1:9869600-9881600	Weak transcription	Fetal Stomach	stomach
34	chr1:9869600-9882000	Weak transcription	NHLF	lung
35	chr1:9869600-9882400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:9869800-9874600	Weak transcription	Fetal Intestine Small	intestine
37	chr1:9869800-9875600	Weak transcription	Spleen	Spleen
38	chr1:9869800-9877000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:9869800-9877000	Weak transcription	Ovary	ovary
40	chr1:9869800-9879600	Weak transcription	GM12878-XiMat	blood
41	chr1:9869800-9882200	Weak transcription	Fetal Thymus	thymus
42	chr1:9869800-9882400	Weak transcription	Thymus	Thymus
43	chr1:9869800-9882600	Weak transcription	Right Atrium	heart
44	chr1:9869800-9882800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:9870000-9875000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:9870000-9881600	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:9870000-9882400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:9870200-9880800	Weak transcription	HMEC	breast
49	chr1:9870400-9880200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:9870600-9875000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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