Variant report

Variant	rs9608667
Chromosome Location	chr22:28540492-28540493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28536612..28538610-chr22:28539278..28541623,2	K562	blood:
2	chr22:28539281..28541367-chr22:28542040..28544765,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs134170	0.84[LWK][hapmap]
rs134185	0.81[LWK][hapmap]
rs134187	0.81[LWK][hapmap]
rs2064360	0.82[YRI][hapmap]
rs2294969	1.00[YRI][hapmap]
rs55916256	0.81[EUR][1000 genomes]
rs5752710	0.86[ASW][hapmap];0.82[YRI][hapmap]
rs5762446	1.00[YRI][hapmap]
rs5762478	1.00[YRI][hapmap]
rs5762492	0.87[LWK][hapmap]
rs5762508	1.00[YRI][hapmap]
rs5762532	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6005754	0.90[JPT][hapmap]
rs715527	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs738995	0.92[CEU][hapmap]
rs9306454	0.92[CEU][hapmap]
rs9613570	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9613574	0.81[CHB][hapmap]

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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv459866	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv588879	chr22:28540492-28753833	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9608667	TTC28	cis	cerebellum	SCAN
rs9608667	TFIP11	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28533600-28542800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr22:28533800-28559000	Weak transcription	Aorta	Aorta
3	chr22:28534200-28545200	Enhancers	Fetal Lung	lung
4	chr22:28534400-28544000	Enhancers	Fetal Brain Male	brain
5	chr22:28534600-28541000	Enhancers	Fetal Stomach	stomach
6	chr22:28535400-28541200	Enhancers	Colon Smooth Muscle	Colon
7	chr22:28535800-28540800	Enhancers	Rectal Smooth Muscle	rectum
8	chr22:28536000-28542200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr22:28536000-28544400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr22:28536200-28542400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr22:28536200-28546600	Weak transcription	Left Ventricle	heart
12	chr22:28536200-28549600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr22:28536400-28542200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr22:28536800-28543800	Enhancers	Fetal Brain Female	brain
15	chr22:28537200-28541000	Enhancers	Fetal Kidney	kidney
16	chr22:28537200-28558800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr22:28537400-28542400	Weak transcription	Right Ventricle	heart
18	chr22:28538000-28542200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr22:28538400-28540600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr22:28538400-28540800	Weak transcription	Lung	lung
21	chr22:28538400-28540800	Enhancers	NHLF	lung
22	chr22:28538400-28543600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr22:28538400-28544800	Weak transcription	Dnd41	blood
24	chr22:28538600-28540600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr22:28538600-28540800	Enhancers	Adipose Nuclei	Adipose
26	chr22:28538800-28541000	Enhancers	Fetal Muscle Leg	muscle
27	chr22:28538800-28549800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr22:28539000-28540800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr22:28539000-28541800	Weak transcription	Brain Substantia Nigra	brain
30	chr22:28539200-28540800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr22:28539200-28540800	Enhancers	HSMMtube	muscle
32	chr22:28539200-28541000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr22:28539200-28541800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr22:28539200-28542400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr22:28539200-28547000	Weak transcription	Fetal Intestine Small	intestine
36	chr22:28539200-28558400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr22:28539400-28542000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr22:28539600-28549800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr22:28539800-28540600	Weak transcription	Small Intestine	intestine
40	chr22:28539800-28541000	Enhancers	Ovary	ovary
41	chr22:28539800-28542000	Weak transcription	Brain Hippocampus Middle	brain
42	chr22:28539800-28542200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr22:28540000-28541000	Enhancers	Right Atrium	heart
44	chr22:28540000-28542000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr22:28540000-28542800	Weak transcription	Osteobl	bone
46	chr22:28540200-28540800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr22:28540200-28540800	Enhancers	Psoas Muscle	Psoas
48	chr22:28540200-28542200	Weak transcription	Brain Angular Gyrus	brain
49	chr22:28540200-28542200	Weak transcription	Brain Anterior Caudate	brain
50	chr22:28540200-28542400	Weak transcription	HSMM	muscle

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