Variant report

Variant	rs2070889
Chromosome Location	chr22:30659566-30659567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30658496..30661192-chr22:30669328..30671945,2	K562	blood:
2	chr22:30658333..30659573-chr22:30782996..30784287,10	MCF-7	breast:
3	chr22:30658407..30662211-chr22:30782039..30784785,6	MCF-7	breast:
4	chr22:30658659..30659608-chr22:30783067..30784163,5	K562	blood:
5	chr22:30658051..30660658-chr22:30661786..30664146,4	K562	blood:
6	chr22:30658735..30661229-chr22:30678360..30682105,3	MCF-7	breast:
7	chr22:30659097..30662032-chr22:30782521..30784593,3	MCF-7	breast:
8	chr22:30657348..30659862-chr22:30818181..30820409,2	K562	blood:
9	chr22:30658717..30661351-chr22:30661980..30663935,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000099999	Chromatin interaction
ENSG00000099985	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs5763918	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6006421	0.92[AMR][1000 genomes]
rs7289095	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];0.81[MKK][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][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	nsv432239	chr22:30580161-30669883	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv914968	chr22:30610570-30693581	Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv914969	chr22:30619599-30691631	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv914971	chr22:30640308-30691631	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv914972	chr22:30640308-30693581	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1062388	chr22:30649179-30711443	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2070889	TPST2	cis	cerebellum	SCAN
rs2070889	THOC5	cis	parietal	SCAN
rs2070889	SMTN	cis	cerebellum	SCAN
rs2070889	SLC5A1	cis	cerebellum	SCAN
rs2070889	MTMR3	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30650000-30661400	Weak transcription	GM12878-XiMat	blood
2	chr22:30653600-30659800	Enhancers	Fetal Thymus	thymus
3	chr22:30654600-30661600	Weak transcription	Thymus	Thymus
4	chr22:30656200-30660000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr22:30656200-30662000	Enhancers	Primary hematopoietic stem cells	blood
6	chr22:30656800-30659800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr22:30656800-30661800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr22:30657200-30659600	Enhancers	Esophagus	oesophagus
9	chr22:30657200-30660000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr22:30658000-30659600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr22:30658200-30661400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr22:30658200-30665200	Transcr. at gene 5' and 3'	Dnd41	blood
13	chr22:30658400-30659600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr22:30658400-30659600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr22:30658400-30659800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr22:30658400-30659800	Enhancers	Placenta	Placenta
17	chr22:30658400-30661400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr22:30658400-30661400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr22:30658600-30659600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr22:30658600-30659800	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr22:30658600-30659800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr22:30659000-30659600	Enhancers	Primary B cells from peripheral blood	blood
23	chr22:30659000-30659600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr22:30659000-30659600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr22:30659000-30659600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr22:30659000-30659600	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr22:30659000-30659600	Active TSS	Colonic Mucosa	Colon
28	chr22:30659000-30659600	Active TSS	Colon Smooth Muscle	Colon
29	chr22:30659000-30659600	Enhancers	Pancreas	Pancrea
30	chr22:30659000-30659600	Flanking Active TSS	A549	lung
31	chr22:30659000-30659600	Enhancers	HSMM	muscle
32	chr22:30659000-30659800	Bivalent Enhancer	Fetal Stomach	stomach
33	chr22:30659000-30659800	Flanking Bivalent TSS/Enh	HepG2	liver
34	chr22:30659000-30659800	Enhancers	HUVEC	blood vessel
35	chr22:30659000-30660200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr22:30659200-30659600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
37	chr22:30659200-30659600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
38	chr22:30659200-30659600	Enhancers	NHDF-Ad	bronchial
39	chr22:30659200-30659800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
40	chr22:30659200-30659800	Enhancers	Fetal Brain Male	brain
41	chr22:30659200-30660000	Enhancers	Spleen	Spleen
42	chr22:30659200-30661200	Weak transcription	Primary T cells from cord blood	blood
43	chr22:30659200-30661400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
44	chr22:30659400-30659600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr22:30659400-30659600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr22:30659400-30659600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr22:30659400-30659600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
48	chr22:30659400-30659600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
49	chr22:30659400-30659600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr22:30659400-30659600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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