Variant report

Variant	rs12254670
Chromosome Location	chr10:27829724-27829725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:27825533..27827174-chr10:27829360..27830870,2	MCF-7	breast:
2	chr10:27814407..27819485-chr10:27827965..27831348,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAB18-3	chr10:27829456-27831143	NONHSAT011910

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10437434	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10508723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10764699	0.86[AFR][1000 genomes]
rs11015830	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015838	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11015842	0.91[AFR][1000 genomes]
rs11015844	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11015848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015851	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11015853	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12242968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12248740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12249534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12253290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12258435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12260532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12261373	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12261690	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12263216	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12267298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2368234	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59498921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60909738	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61486615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9651381	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550241	chr10:27569521-28025771	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1045257	chr10:27572440-27926946	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1053952	chr10:27659365-27915029	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 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	chr10:27794400-27837400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:27795800-27832600	Weak transcription	Small Intestine	intestine
3	chr10:27803400-27830800	Weak transcription	Hela-S3	cervix
4	chr10:27814200-27836000	Weak transcription	Brain Germinal Matrix	brain
5	chr10:27815000-27831000	Weak transcription	Fetal Heart	heart
6	chr10:27815000-27834400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr10:27815600-27831600	Weak transcription	Psoas Muscle	Psoas
8	chr10:27818800-27830800	Weak transcription	Stomach Mucosa	stomach
9	chr10:27820400-27835200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr10:27821800-27830000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr10:27822200-27830000	Strong transcription	Primary B cells from cord blood	blood
12	chr10:27822200-27835200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr10:27822400-27831600	Strong transcription	Osteobl	bone
14	chr10:27822400-27832000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr10:27822600-27830200	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr10:27822600-27832400	Strong transcription	Adipose Nuclei	Adipose
17	chr10:27822600-27832400	Strong transcription	Dnd41	blood
18	chr10:27822600-27832800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr10:27823000-27836200	Weak transcription	Fetal Brain Female	brain
20	chr10:27823000-27838200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr10:27823400-27836600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr10:27823600-27831600	Weak transcription	HUVEC	blood vessel
23	chr10:27823600-27834800	Weak transcription	Colon Smooth Muscle	Colon
24	chr10:27823600-27838200	Weak transcription	Pancreas	Pancrea
25	chr10:27823800-27830800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr10:27824000-27830000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr10:27824000-27833800	Weak transcription	Brain Anterior Caudate	brain
28	chr10:27824400-27834000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr10:27824400-27835800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:27824400-27836200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr10:27824600-27829800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr10:27824600-27831000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr10:27824600-27833400	Weak transcription	Brain Angular Gyrus	brain
34	chr10:27824600-27834400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr10:27824600-27835200	Weak transcription	Colonic Mucosa	Colon
36	chr10:27824600-27836000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr10:27824600-27836400	Weak transcription	Fetal Kidney	kidney
38	chr10:27824600-27838000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr10:27824800-27836600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr10:27825000-27836600	Weak transcription	Gastric	stomach
41	chr10:27825600-27831000	Weak transcription	Fetal Intestine Small	intestine
42	chr10:27825600-27831800	Weak transcription	Fetal Stomach	stomach
43	chr10:27825600-27834200	Weak transcription	Lung	lung
44	chr10:27825600-27835200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr10:27825800-27831600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr10:27825800-27834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr10:27826000-27831400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr10:27826200-27831600	Weak transcription	Esophagus	oesophagus
49	chr10:27826200-27833400	Weak transcription	Brain Hippocampus Middle	brain
50	chr10:27826200-27834200	Weak transcription	Right Ventricle	heart

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