Variant report

Variant	rs12688688
Chromosome Location	chrX:138856248-138856249
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10126150	0.86[YRI][hapmap]
rs12389012	0.86[YRI][hapmap]
rs12687833	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs12688014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12688450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12688705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12689725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1338059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1361155	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1415887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17281969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17281990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17282011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17282039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17282067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17282081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17328640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17328647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17328703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17328709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1890241	0.86[YRI][hapmap]
rs2183251	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs2252290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2485721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2485722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2485724	1.00[CHB][hapmap]
rs2485728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2485729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2485732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2485733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2491005	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2491006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2491009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2497266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2497273	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2497274	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2497277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2497280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2497281	1.00[CHB][hapmap]
rs2497282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2497284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2772192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2772194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2805901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2805902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4239992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4363374	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs4824924	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs5908152	0.81[YRI][hapmap]
rs5908669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5908746	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs5953621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5953643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5953692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs5953748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5953790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs5953791	0.81[YRI][hapmap]
rs5953812	0.81[YRI][hapmap]
rs5954529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5954540	0.86[YRI][hapmap]
rs5954556	0.81[YRI][hapmap]
rs5954562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5954594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5954768	0.86[YRI][hapmap]
rs5954897	0.81[YRI][hapmap]
rs5954997	0.86[YRI][hapmap]
rs5955049	0.81[YRI][hapmap]
rs6528650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6528651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6635906	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6635927	0.86[YRI][hapmap]
rs6654371	1.00[CEU][hapmap]
rs7061584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7885696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:138806800-138866800	Weak transcription	Left Ventricle	heart
2	chrX:138807200-138858200	Weak transcription	Primary B cells from cord blood	blood
3	chrX:138814000-138883600	Weak transcription	Gastric	stomach
4	chrX:138818600-138857600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chrX:138821400-138870800	Weak transcription	HSMMtube	muscle
6	chrX:138822000-138857000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chrX:138822200-138882600	Weak transcription	Osteobl	bone
8	chrX:138824800-138870000	Weak transcription	Colonic Mucosa	Colon
9	chrX:138827000-138895400	Weak transcription	Hela-S3	cervix
10	chrX:138827400-138888800	Weak transcription	Small Intestine	intestine
11	chrX:138829600-138859200	Weak transcription	HepG2	liver
12	chrX:138833000-138907400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chrX:138841000-138870000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chrX:138841400-138882600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chrX:138841800-138898600	Weak transcription	HUVEC	blood vessel
16	chrX:138842800-138879600	Weak transcription	Brain Germinal Matrix	brain
17	chrX:138844800-138857000	Weak transcription	Stomach Smooth Muscle	stomach
18	chrX:138844800-138881400	Weak transcription	Brain Hippocampus Middle	brain
19	chrX:138845400-138870400	Weak transcription	NH-A	brain
20	chrX:138845800-138857800	Weak transcription	Spleen	Spleen
21	chrX:138847600-138875800	Weak transcription	Fetal Kidney	kidney
22	chrX:138847800-138888600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chrX:138847800-138899400	Weak transcription	Aorta	Aorta
24	chrX:138848000-138870000	Weak transcription	Fetal Lung	lung
25	chrX:138848400-138883400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chrX:138848600-138867000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chrX:138848600-138897200	Weak transcription	Brain Anterior Caudate	brain
28	chrX:138849200-138868600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chrX:138849200-138888200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chrX:138849400-138867600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chrX:138849600-138879200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chrX:138849600-138885800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chrX:138849600-138898600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chrX:138850000-138868600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chrX:138850200-138885000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chrX:138851600-138870200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chrX:138851800-138858800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chrX:138851800-138859000	Strong transcription	Liver	Liver
39	chrX:138852000-138867000	Weak transcription	Primary hematopoietic stem cells	blood
40	chrX:138852600-138858600	Strong transcription	Fetal Intestine Large	intestine
41	chrX:138852600-138890600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chrX:138852800-138857000	Strong transcription	Fetal Thymus	thymus
43	chrX:138853000-138908000	Weak transcription	A549	lung
44	chrX:138853200-138870000	Weak transcription	Adipose Nuclei	Adipose
45	chrX:138853200-138873200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chrX:138853800-138858000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chrX:138854200-138857400	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chrX:138854200-138858600	Strong transcription	Primary B cells from peripheral blood	blood
49	chrX:138854200-138858600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chrX:138854400-138856400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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