Variant report

Variant	rs12787498
Chromosome Location	chr11:108584937-108584938
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10732846	0.97[EUR][1000 genomes]
rs12788182	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12799569	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12807367	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466502	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531470	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947928	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947929	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061680	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126570	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615721	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615734	0.82[EUR][1000 genomes]
rs2615735	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2615738	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2615742	0.85[EUR][1000 genomes]
rs2726876	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2726880	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2726887	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2726891	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34746018	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35234597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35396330	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3951111	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4754342	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6589029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68161639	0.86[AMR][1000 genomes]
rs7124142	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129535	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71489910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71489912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71489921	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71489923	0.85[EUR][1000 genomes]
rs73005544	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931638	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052254	chr11:108122683-108845008	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv541164	chr11:108122683-108845008	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv898386	chr11:108409442-108831875	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv898388	chr11:108440814-108724639	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv832264	chr11:108449613-108623720	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:108564800-108595400	Weak transcription	Hela-S3	cervix
2	chr11:108572000-108590400	Weak transcription	Stomach Mucosa	stomach
3	chr11:108574800-108586800	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:108575400-108599400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:108577200-108586200	Strong transcription	HSMM	muscle
6	chr11:108577600-108604400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:108578000-108604400	Weak transcription	Small Intestine	intestine
8	chr11:108578200-108596000	Weak transcription	Right Ventricle	heart
9	chr11:108578200-108604400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:108578800-108596800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:108578800-108604000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr11:108578800-108604000	Weak transcription	Colon Smooth Muscle	Colon
13	chr11:108578800-108604200	Weak transcription	NHLF	lung
14	chr11:108578800-108604600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr11:108578800-108614400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr11:108579000-108586200	Strong transcription	Dnd41	blood
17	chr11:108579000-108595600	Weak transcription	Colonic Mucosa	Colon
18	chr11:108579200-108585400	Weak transcription	Fetal Thymus	thymus
19	chr11:108579200-108604000	Weak transcription	HUVEC	blood vessel
20	chr11:108579600-108600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:108579800-108595000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr11:108579800-108604200	Weak transcription	Psoas Muscle	Psoas
23	chr11:108580000-108587200	Strong transcription	Primary T cells from cord blood	blood
24	chr11:108580000-108593400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr11:108580000-108593800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr11:108580000-108603800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr11:108580200-108586800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:108580200-108593200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr11:108580200-108593200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr11:108580200-108593400	Weak transcription	K562	blood
31	chr11:108580200-108593600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr11:108580800-108590200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr11:108581000-108585800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr11:108581000-108604200	Weak transcription	Fetal Heart	heart
35	chr11:108581200-108604200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr11:108581600-108588200	Weak transcription	Fetal Intestine Large	intestine
37	chr11:108581600-108593600	Weak transcription	Placenta	Placenta
38	chr11:108581600-108626600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:108581800-108585800	Weak transcription	HepG2	liver
40	chr11:108581800-108586000	Weak transcription	HMEC	breast
41	chr11:108581800-108586800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr11:108581800-108586800	Weak transcription	Fetal Stomach	stomach
43	chr11:108581800-108588000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr11:108581800-108590600	Weak transcription	Left Ventricle	heart
45	chr11:108581800-108592600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:108581800-108592600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr11:108581800-108593600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr11:108581800-108593800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:108581800-108593800	Weak transcription	HSMMtube	muscle
50	chr11:108581800-108595000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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