Variant report

Variant	rs12689199
Chromosome Location	chrX:138827376-138827377
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chrX:138826048..138827648-chrX:138828172..138829873,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12688014	1.00[GIH][hapmap];0.83[MEX][hapmap]
rs12688450	1.00[GIH][hapmap];0.83[MEX][hapmap]
rs12688705	1.00[GIH][hapmap];0.83[MEX][hapmap]
rs1361155	0.83[GIH][hapmap]
rs1415887	1.00[GIH][hapmap]
rs17281969	1.00[GIH][hapmap];0.83[MEX][hapmap]
rs17281990	1.00[GIH][hapmap];0.83[MEX][hapmap]
rs17282011	1.00[GIH][hapmap]
rs17282067	1.00[GIH][hapmap];0.83[MEX][hapmap]
rs17328640	1.00[GIH][hapmap];0.83[MEX][hapmap]
rs17328647	1.00[GIH][hapmap]
rs17328703	1.00[GIH][hapmap];0.83[MEX][hapmap]
rs17328709	1.00[GIH][hapmap];0.91[MEX][hapmap]
rs2485722	0.83[GIH][hapmap]
rs2485729	1.00[GIH][hapmap]
rs2485732	1.00[GIH][hapmap]
rs2491005	1.00[GIH][hapmap]
rs2491006	1.00[GIH][hapmap]
rs2491009	1.00[GIH][hapmap]
rs2497266	1.00[GIH][hapmap]
rs2497274	1.00[GIH][hapmap]
rs2497277	1.00[GIH][hapmap]
rs2497282	0.83[GIH][hapmap]
rs2497284	1.00[GIH][hapmap]
rs2772194	1.00[GIH][hapmap]
rs2805901	1.00[GIH][hapmap]
rs3747365	0.81[MEX][hapmap]
rs4239992	1.00[GIH][hapmap]
rs4824924	1.00[GIH][hapmap]
rs5908669	1.00[GIH][hapmap]
rs5908746	1.00[GIH][hapmap]
rs5953621	1.00[GIH][hapmap]
rs5953643	1.00[GIH][hapmap]
rs5953692	1.00[GIH][hapmap];0.83[MEX][hapmap]
rs5953790	1.00[GIH][hapmap]
rs5954529	1.00[GIH][hapmap]
rs6528650	1.00[GIH][hapmap]
rs6528651	1.00[GIH][hapmap]
rs6654371	0.83[GIH][hapmap]
rs7061584	1.00[GIH][hapmap]
rs7885696	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532936	chrX:138687855-139384681	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
2	nsv491760	chrX:138780768-139283477	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
3	nsv7116	chrX:138815720-138851105	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:138802200-138836600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chrX:138804800-138832000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chrX:138805200-138829200	Weak transcription	Duodenum Mucosa	Duodenum
4	chrX:138805400-138835200	Weak transcription	Primary hematopoietic stem cells	blood
5	chrX:138806600-138836400	Weak transcription	Dnd41	blood
6	chrX:138806800-138866800	Weak transcription	Left Ventricle	heart
7	chrX:138807200-138858200	Weak transcription	Primary B cells from cord blood	blood
8	chrX:138807600-138831200	Weak transcription	Fetal Muscle Trunk	muscle
9	chrX:138807800-138832400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chrX:138808200-138835600	Weak transcription	Fetal Stomach	stomach
11	chrX:138808400-138832600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chrX:138809000-138836000	Weak transcription	Adipose Nuclei	Adipose
13	chrX:138810000-138835000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chrX:138810600-138840400	Weak transcription	K562	blood
15	chrX:138811200-138834800	Weak transcription	Spleen	Spleen
16	chrX:138812200-138832200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chrX:138812800-138831200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chrX:138812800-138835600	Weak transcription	Fetal Thymus	thymus
19	chrX:138813600-138833400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chrX:138814000-138883600	Weak transcription	Gastric	stomach
21	chrX:138814200-138848400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chrX:138815200-138849000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chrX:138815400-138829200	Weak transcription	HepG2	liver
24	chrX:138815800-138854200	Weak transcription	Thymus	Thymus
25	chrX:138816800-138835800	Weak transcription	Brain Germinal Matrix	brain
26	chrX:138817400-138832000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chrX:138818200-138836600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chrX:138818600-138830600	Weak transcription	Psoas Muscle	Psoas
29	chrX:138818600-138857600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chrX:138819200-138834000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chrX:138819400-138834800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chrX:138819800-138832200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chrX:138819800-138848400	Weak transcription	Fetal Intestine Large	intestine
34	chrX:138820200-138832800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chrX:138821000-138829400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chrX:138821000-138854600	Weak transcription	Ovary	ovary
37	chrX:138821400-138829400	Weak transcription	HMEC	breast
38	chrX:138821400-138836600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chrX:138821400-138838000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chrX:138821400-138848200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chrX:138821400-138854000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chrX:138821400-138870800	Weak transcription	HSMMtube	muscle
43	chrX:138821600-138829600	Weak transcription	Primary T cells from cord blood	blood
44	chrX:138821600-138830000	Weak transcription	GM12878-XiMat	blood
45	chrX:138821800-138833800	Weak transcription	NH-A	brain
46	chrX:138821800-138834200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chrX:138822000-138836600	Weak transcription	Fetal Intestine Small	intestine
48	chrX:138822000-138857000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chrX:138822200-138882600	Weak transcription	Osteobl	bone
50	chrX:138822400-138828000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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