Variant report

Variant	rs9425311
Chromosome Location	chr1:172388778-172388779
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172385755..172389106-chr1:172391207..172393719,3	K562	blood:
2	chr1:172375496..172379926-chr1:172385834..172389157,4	MCF-7	breast:
3	chr1:172381987..172384677-chr1:172388260..172389798,2	K562	blood:

Variant related genes	Relation type
ENSG00000135845	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1063412	0.87[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs10752946	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.96[ASN][1000 genomes]
rs10752957	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10798005	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10798026	1.00[ASW][hapmap];0.91[MKK][hapmap]
rs10911786	1.00[ASW][hapmap];0.86[MKK][hapmap]
rs11484605	0.96[ASN][1000 genomes]
rs12076560	0.85[ASN][1000 genomes]
rs13932	1.00[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs2269613	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs2269614	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs2269615	1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs2269616	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2285170	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs2285171	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs2285172	0.81[ASN][1000 genomes]
rs2285173	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs2285174	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs2285175	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs2285176	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs2301455	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs2422141	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2901656	0.96[CEU][hapmap]
rs3213563	0.83[ASN][1000 genomes]
rs3937046	1.00[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs4916186	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916258	0.83[ASN][1000 genomes]
rs60302909	0.80[ASN][1000 genomes]
rs6424923	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs6658843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6673869	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs6674073	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs6689377	0.81[ASN][1000 genomes]
rs6691993	0.92[CEU][hapmap]
rs6699095	0.96[CEU][hapmap]
rs6702667	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7411767	0.96[ASN][1000 genomes]
rs7516301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528296	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs929098	0.81[ASN][1000 genomes]
rs9425308	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs9425313	0.96[ASN][1000 genomes]
rs9425316	0.96[ASN][1000 genomes]
rs9425598	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9425600	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9425601	0.96[ASN][1000 genomes]
rs9425602	0.98[ASN][1000 genomes]
rs9425604	0.98[ASN][1000 genomes]
rs9425606	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9425311	SNORD79	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172368400-172390800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:172373000-172390800	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:172373000-172390800	Weak transcription	Brain Substantia Nigra	brain
4	chr1:172373000-172411800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:172382200-172390800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:172384400-172398400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:172385000-172391600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:172385800-172391000	Weak transcription	Fetal Lung	lung
9	chr1:172385800-172411000	Weak transcription	Fetal Stomach	stomach
10	chr1:172386000-172391200	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:172386800-172390800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:172386800-172390800	Weak transcription	Psoas Muscle	Psoas
13	chr1:172386800-172391200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:172387000-172389800	Weak transcription	Fetal Thymus	thymus
15	chr1:172387200-172390800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:172387200-172390800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:172387200-172392200	Enhancers	Primary T cells from cord blood	blood
18	chr1:172387400-172389800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:172387400-172390600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:172387400-172390600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:172387400-172391000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:172387600-172389800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:172387600-172392400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:172387600-172392400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:172388000-172388800	Enhancers	HMEC	breast
26	chr1:172388400-172388800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:172388400-172389000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:172388600-172388800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr1:172388600-172392200	Weak transcription	NHEK	skin

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