Variant report

Variant	rs12266049
Chromosome Location	chr10:90656701-90656702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr10:90656686-90657807	HCT-116	colon:	n/a	n/a
2	EP300	chr10:90656674-90657686	SK-N-SH	brain:	n/a	chr10:90657116-90657129
3	KAP1	chr10:90656033-90657749	U2OS	brain:	n/a	n/a
4	KAP1	chr10:90656110-90657745	HEK293	kidney:	n/a	n/a
5	GATA3	chr10:90656666-90657927	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr10:90656631-90657739	SK-N-SH	brain:	n/a	n/a
7	STAT1	chr10:90656033-90657545	Hela-S3	cervix:	n/a	chr10:90656641-90656652 chr10:90656268-90656279 chr10:90656270-90656279 chr10:90656269-90656278
8	POLR2A	chr10:90656107-90658222	GM12891	blood:	n/a	n/a
9	SP1	chr10:90655989-90657715	HCT-116	colon:	n/a	chr10:90657194-90657201 chr10:90656309-90656330

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90655598..90657313-chr10:90680167..90681705,2	K562	blood:

Variant related genes	Relation type
STAMBPL1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10509558	0.86[YRI][hapmap]
rs10509559	0.88[YRI][hapmap]
rs11202882	0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11202884	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12240659	1.00[AMR][1000 genomes]
rs12242274	0.93[YRI][hapmap]
rs12243282	0.94[YRI][hapmap]
rs12245057	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs12245122	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs12258025	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs12260182	0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12260572	0.94[YRI][hapmap]
rs12262692	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12266993	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs17114024	0.88[YRI][hapmap]
rs2231785	0.88[YRI][hapmap]
rs2231786	0.86[YRI][hapmap]
rs3898173	0.88[YRI][hapmap]
rs3898174	0.88[YRI][hapmap]
rs58014217	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7070713	1.00[AMR][1000 genomes]
rs9804254	0.87[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 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	chr10:90641400-90658600	Weak transcription	Brain Angular Gyrus	brain
2	chr10:90641800-90661800	Weak transcription	Thymus	Thymus
3	chr10:90642000-90684800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr10:90642000-90686400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr10:90646800-90656800	Weak transcription	Psoas Muscle	Psoas
6	chr10:90647400-90675200	Weak transcription	Spleen	Spleen
7	chr10:90647400-90681000	Weak transcription	Aorta	Aorta
8	chr10:90652000-90658200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr10:90652400-90656800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr10:90652400-90663000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr10:90652600-90656800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr10:90652600-90656800	Weak transcription	NH-A	brain
13	chr10:90652600-90657000	Weak transcription	Brain Substantia Nigra	brain
14	chr10:90652600-90660800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:90652600-90661400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:90652800-90661200	Weak transcription	NHEK	skin
17	chr10:90652800-90661800	Weak transcription	HMEC	breast
18	chr10:90653600-90657600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr10:90653600-90659200	Enhancers	Fetal Intestine Small	intestine
20	chr10:90653800-90657000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:90654000-90687400	Weak transcription	Right Ventricle	heart
22	chr10:90654200-90661800	Enhancers	Fetal Intestine Large	intestine
23	chr10:90654600-90657600	Enhancers	Liver	Liver
24	chr10:90654600-90658800	Weak transcription	Primary B cells from cord blood	blood
25	chr10:90654800-90656800	Enhancers	HepG2	liver
26	chr10:90654800-90657200	Genic enhancers	GM12878-XiMat	blood
27	chr10:90654800-90657400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr10:90655000-90659000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr10:90655200-90657000	Genic enhancers	Primary T cells from cord blood	blood
30	chr10:90655200-90675200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr10:90655200-90701400	Weak transcription	Gastric	stomach
32	chr10:90655400-90657000	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr10:90655400-90657200	Enhancers	Osteobl	bone
34	chr10:90655400-90657400	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr10:90655400-90657600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr10:90655400-90658800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr10:90655400-90661200	Weak transcription	Fetal Thymus	thymus
38	chr10:90655800-90657600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr10:90655800-90658000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr10:90655800-90658600	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr10:90655800-90658800	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr10:90655800-90660600	Weak transcription	Dnd41	blood
43	chr10:90656000-90657400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr10:90656000-90657600	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr10:90656000-90657600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr10:90656000-90657600	Enhancers	Brain Hippocampus Middle	brain
47	chr10:90656000-90657800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr10:90656000-90658000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr10:90656000-90658000	Enhancers	Fetal Lung	lung
50	chr10:90656000-90658000	Enhancers	Stomach Mucosa	stomach

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