Variant report

Variant	rs714027
Chromosome Location	chr22:30577771-30577772
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1003342	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1548389	0.81[JPT][hapmap]
rs193477	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412970	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2412971	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2412975	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4823073	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4823074	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4823075	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4823077	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763767	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997579	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6006356	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs713875	0.89[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs757024	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv588884	chr22:30494371-30590026	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv527188	chr22:30529741-30581722	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv524628	chr22:30575163-30581722	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs714027	TTC28	cis	cerebellum	SCAN
rs714027	CABP7	cis	cerebellum	SCAN
rs714027	NEFH	cis	cerebellum	SCAN
rs714027	MTMR3	cis	parietal	SCAN
rs714027	ASCC2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30572800-30578000	Weak transcription	Spleen	Spleen
2	chr22:30572800-30579000	Weak transcription	Fetal Brain Male	brain
3	chr22:30573600-30579400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr22:30574400-30583600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr22:30574800-30579400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr22:30575000-30579800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr22:30575000-30583600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr22:30575200-30578400	Weak transcription	Fetal Thymus	thymus
9	chr22:30575200-30580000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr22:30575400-30579000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr22:30575400-30584400	Enhancers	Primary hematopoietic stem cells	blood
12	chr22:30575400-30584800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr22:30575600-30579800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr22:30575600-30583400	Weak transcription	Primary T cells from cord blood	blood
15	chr22:30575600-30584600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr22:30575800-30577800	Enhancers	Primary B cells from cord blood	blood
17	chr22:30575800-30578400	Weak transcription	Dnd41	blood
18	chr22:30576200-30588000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr22:30576400-30579800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr22:30577200-30578600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr22:30577200-30580200	Enhancers	HepG2	liver
22	chr22:30577400-30578600	Enhancers	Duodenum Mucosa	Duodenum
23	chr22:30577400-30578600	Enhancers	Stomach Mucosa	stomach
24	chr22:30577400-30578800	Enhancers	Fetal Intestine Small	intestine
25	chr22:30577600-30577800	Enhancers	Thymus	Thymus
26	chr22:30577600-30578000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr22:30577600-30578200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr22:30577600-30578400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr22:30577600-30578600	Bivalent Enhancer	HUVEC	blood vessel
30	chr22:30577600-30578800	Enhancers	K562	blood
31	chr22:30577600-30579000	Enhancers	Fetal Intestine Large	intestine
32	chr22:30577600-30580200	Enhancers	Fetal Lung	lung
33	chr22:30577600-30589600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr22:30577600-30591400	Enhancers	A549	lung

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