Variant report

Variant	rs12898461
Chromosome Location	chr15:49539043-49539044
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	chr15:49538461..49540714-chr15:49541925..49544059,3	K562	blood:
2	chr15:49535482..49538280-chr15:49538929..49540490,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11070685	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[EUR][1000 genomes]
rs12232354	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12591799	1.00[YRI][hapmap]
rs12592177	1.00[YRI][hapmap]
rs12592296	1.00[YRI][hapmap]
rs12593068	1.00[YRI][hapmap]
rs12594154	1.00[YRI][hapmap]
rs12594827	1.00[YRI][hapmap]
rs12898877	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903992	0.89[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs12910584	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12914592	0.88[CEU][hapmap]
rs12915792	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12916078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1429555	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1583060	0.89[CEU][hapmap]
rs16962414	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs16962418	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs16962419	0.89[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs16962434	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34505850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35274049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809495	1.00[YRI][hapmap]
rs478500	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs577614	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[EUR][1000 genomes]
rs6493351	0.90[EUR][1000 genomes]
rs6493366	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs6493367	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs71394957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs71467666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71467668	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166491	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7169304	0.93[ASN][1000 genomes]
rs7177959	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[EUR][1000 genomes]
rs8026364	0.87[EUR][1000 genomes]
rs8029538	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8036293	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8040116	0.89[CEU][hapmap];0.84[CHB][hapmap];0.90[EUR][1000 genomes]
rs9806362	0.87[EUR][1000 genomes]

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	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv569340	chr15:49529302-49547735	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv569341	chr15:49529302-49547790	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv569342	chr15:49529302-49549943	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv569343	chr15:49531192-49547790	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv569344	chr15:49534702-49546105	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv569345	chr15:49534702-49546939	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv569346	chr15:49534702-49547790	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv569347	chr15:49534702-49549943	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
2	chr15:49492000-49539400	Weak transcription	Small Intestine	intestine
3	chr15:49510000-49541800	Weak transcription	NHEK	skin
4	chr15:49518000-49541000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:49518200-49548600	Weak transcription	Aorta	Aorta
6	chr15:49518600-49557600	Weak transcription	Esophagus	oesophagus
7	chr15:49518800-49539200	Weak transcription	Ovary	ovary
8	chr15:49520400-49595600	Weak transcription	Right Ventricle	heart
9	chr15:49522000-49540400	Weak transcription	Stomach Mucosa	stomach
10	chr15:49522400-49559400	Weak transcription	Pancreas	Pancrea
11	chr15:49523800-49540200	Weak transcription	Spleen	Spleen
12	chr15:49524600-49539200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:49524600-49544800	Weak transcription	Lung	lung
14	chr15:49528000-49539600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:49528000-49576000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:49528400-49547800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr15:49529200-49550600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:49529400-49539800	Weak transcription	Brain Hippocampus Middle	brain
19	chr15:49529400-49540200	Weak transcription	Fetal Brain Female	brain
20	chr15:49529400-49544200	Weak transcription	Brain Anterior Caudate	brain
21	chr15:49529400-49545600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:49529600-49541600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:49530000-49539200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:49531000-49540400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr15:49531000-49540600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:49531000-49542800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr15:49531200-49540000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:49531600-49539400	Weak transcription	Psoas Muscle	Psoas
29	chr15:49531800-49539400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:49532000-49545000	Weak transcription	Fetal Thymus	thymus
31	chr15:49532200-49539200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:49532200-49539400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:49532200-49542600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr15:49532800-49545400	Weak transcription	HUVEC	blood vessel
35	chr15:49533000-49541400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr15:49533400-49548200	Weak transcription	HMEC	breast
37	chr15:49533800-49576200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:49534600-49539600	Strong transcription	Primary hematopoietic stem cells	blood
39	chr15:49535200-49540000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:49535400-49539600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:49535600-49541200	Weak transcription	Fetal Kidney	kidney
42	chr15:49535600-49557000	Weak transcription	Fetal Intestine Small	intestine
43	chr15:49535600-49564600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr15:49535600-49574200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr15:49535600-49574200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr15:49535800-49539600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr15:49535800-49539600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:49535800-49540000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:49535800-49540000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:49535800-49540400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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