Variant report

Variant	rs10166357
Chromosome Location	chr2:74230656-74230657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74153966..74155499-chr2:74229025..74232283,3	K562	blood:
2	chr2:74230315..74232342-chr2:74308990..74310979,2	K562	blood:
3	chr2:74229598..74231793-chr2:74423826..74425705,2	MCF-7	breast:
4	chr2:74153007..74155466-chr2:74228011..74231907,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TET3-3	chr2:74229333-74230678	ucscGeneNc_uc002ske_2

Variant related genes	Relation type
ENSG00000114956	Chromatin interaction
ENSG00000065911	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10165243	0.81[EUR][1000 genomes]
rs10206797	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12713802	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13391252	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13391360	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13391722	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13404452	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13416937	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28534414	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28569001	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34363691	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34961871	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35259799	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35972889	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4241258	0.84[EUR][1000 genomes]
rs7581252	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7608044	0.88[EUR][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	nsv1011177	chr2:74167343-74239905	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv3584956	chr2:74197109-74317135	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv818048	chr2:74225434-74313080	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3436825	chr2:74228469-74231017	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3394982	chr2:74229169-74232017	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74226200-74232400	Weak transcription	Hela-S3	cervix
2	chr2:74228800-74231000	Weak transcription	Small Intestine	intestine
3	chr2:74228800-74231200	Active TSS	Psoas Muscle	Psoas
4	chr2:74229200-74230800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr2:74229200-74231000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr2:74229200-74231000	Active TSS	Brain Cingulate Gyrus	brain
7	chr2:74229200-74231000	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr2:74229400-74230800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:74229400-74230800	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr2:74229400-74230800	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr2:74229400-74230800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:74229400-74230800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:74229400-74230800	Active TSS	Brain Hippocampus Middle	brain
14	chr2:74229400-74230800	Active TSS	Fetal Lung	lung
15	chr2:74229400-74230800	Active TSS	NHLF	lung
16	chr2:74229400-74231000	Active TSS	H1 Cell Line	embryonic stem cell
17	chr2:74229400-74231000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:74229400-74231000	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr2:74229400-74231000	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr2:74229400-74231000	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr2:74229400-74231000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:74229400-74231000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr2:74229400-74231000	Active TSS	Brain Angular Gyrus	brain
24	chr2:74229400-74231000	Active TSS	Brain Anterior Caudate	brain
25	chr2:74229400-74231000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:74229400-74231000	Active TSS	Brain Substantia Nigra	brain
27	chr2:74229400-74231000	Active TSS	Ovary	ovary
28	chr2:74229400-74231000	Active TSS	K562	blood
29	chr2:74229400-74231200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:74229400-74231200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:74229600-74230800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:74229600-74231000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr2:74229600-74231000	Active TSS	HSMMtube	muscle
34	chr2:74229600-74231200	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr2:74229800-74230800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:74230000-74230800	Flanking Active TSS	Thymus	Thymus
37	chr2:74230000-74231000	Active TSS	Fetal Kidney	kidney
38	chr2:74230200-74231000	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr2:74230200-74231200	Enhancers	Lung	lung
40	chr2:74230200-74231800	Flanking Active TSS	Osteobl	bone
41	chr2:74230400-74230800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:74230400-74230800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:74230400-74230800	Active TSS	Muscle Satellite Cultured Cells	--
44	chr2:74230400-74230800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:74230400-74230800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:74230400-74230800	Active TSS	Brain Germinal Matrix	brain
47	chr2:74230400-74230800	Enhancers	Fetal Brain Male	brain
48	chr2:74230400-74231000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:74230400-74231000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:74230400-74231000	Enhancers	Primary B cells from cord blood	blood

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