Variant report

Variant	rs12260887
Chromosome Location	chr10:52267903-52267904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52227035..52229845-chr10:52267079..52268728,2	MCF-7	breast:
2	chr10:52266589..52268433-chr10:52270760..52273217,2	K562	blood:
3	chr10:52264059..52268097-chr10:52270623..52273217,5	K562	blood:
4	chr10:52227177..52229638-chr10:52267267..52268794,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11005626	0.80[YRI][hapmap]
rs11005780	0.83[AFR][1000 genomes]
rs11005832	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs11005910	0.85[AFR][1000 genomes]
rs11005972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1203375	0.85[YRI][hapmap]
rs1203382	0.95[YRI][hapmap]
rs1203386	0.95[YRI][hapmap]
rs1203394	0.95[YRI][hapmap]
rs1203407	0.90[YRI][hapmap]
rs1203409	0.83[YRI][hapmap]
rs1203410	0.85[YRI][hapmap]
rs1203421	0.85[YRI][hapmap]
rs12241198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12246361	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs12261287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12263463	0.85[AFR][1000 genomes]
rs12264511	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12264817	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs12267134	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7068377	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7895767	0.85[AFR][1000 genomes]
rs920136	0.85[YRI][hapmap]
rs9988708	0.85[LWK][hapmap];0.85[YRI][hapmap]

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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv895391	chr10:52260398-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv895392	chr10:52263910-52291608	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv467193	chr10:52265265-52289664	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv550855	chr10:52265265-52289664	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52247000-52271200	Weak transcription	Colon Smooth Muscle	Colon
2	chr10:52253800-52268200	Weak transcription	Fetal Intestine Small	intestine
3	chr10:52258000-52271800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr10:52261000-52268200	Weak transcription	Gastric	stomach
5	chr10:52261800-52271400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:52262000-52270800	Weak transcription	HSMMtube	muscle
7	chr10:52262200-52271200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr10:52262200-52287200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:52262400-52268600	Weak transcription	A549	lung
10	chr10:52262400-52270600	Weak transcription	Primary T cells from cord blood	blood
11	chr10:52262400-52271800	Weak transcription	Fetal Stomach	stomach
12	chr10:52262400-52272600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr10:52262600-52271200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr10:52262800-52273000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr10:52263800-52271400	Weak transcription	Placenta	Placenta
16	chr10:52263800-52271800	Weak transcription	Esophagus	oesophagus
17	chr10:52264000-52268000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr10:52264000-52268000	Weak transcription	Stomach Mucosa	stomach
19	chr10:52264200-52270800	Weak transcription	K562	blood
20	chr10:52264400-52269600	Weak transcription	Hela-S3	cervix
21	chr10:52264600-52271600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr10:52264800-52271000	Weak transcription	NHEK	skin
23	chr10:52265000-52271200	Enhancers	Brain Cingulate Gyrus	brain
24	chr10:52265000-52272400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr10:52265200-52268800	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr10:52265400-52270000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr10:52265400-52270400	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr10:52265400-52273200	Enhancers	Brain Angular Gyrus	brain
29	chr10:52266000-52268400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr10:52266200-52272800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr10:52266400-52268000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr10:52266400-52268200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr10:52266400-52268200	Enhancers	Left Ventricle	heart
34	chr10:52266400-52268400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr10:52266400-52272800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:52266400-52272800	Enhancers	HepG2	liver
37	chr10:52266600-52268200	Enhancers	H1 Cell Line	embryonic stem cell
38	chr10:52266600-52268200	Enhancers	H9 Cell Line	embryonic stem cell
39	chr10:52266600-52268800	Enhancers	Primary T cells fromperipheralblood	blood
40	chr10:52266600-52268800	Enhancers	Fetal Muscle Leg	muscle
41	chr10:52266600-52268800	Enhancers	Pancreas	Pancrea
42	chr10:52266800-52268000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr10:52266800-52268800	Strong transcription	Primary B cells from cord blood	blood
44	chr10:52266800-52268800	Enhancers	Right Atrium	heart
45	chr10:52266800-52271200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr10:52266800-52282400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr10:52267000-52268000	Weak transcription	Liver	Liver
48	chr10:52267000-52268800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr10:52267000-52268800	Enhancers	Psoas Muscle	Psoas
50	chr10:52267000-52269000	Enhancers	Fetal Kidney	kidney

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