Variant report

Variant	rs6702667
Chromosome Location	chr1:172400484-172400485
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172398801..172400537-chr1:172417664..172420228,2	K562	blood:
2	chr1:172398685..172401320-chr1:172498374..172501094,2	MCF-7	breast:
3	chr1:172397089..172401032-chr1:172412108..172414931,5	K562	blood:
4	chr1:171971874..171974567-chr1:172398911..172400668,2	MCF-7	breast:
5	chr1:172399642..172402541-chr1:172412542..172414474,2	MCF-7	breast:
6	chr1:172393961..172396841-chr1:172398956..172400533,2	K562	blood:

Variant related genes	Relation type
ENSG00000180999	Chromatin interaction
ENSG00000135845	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1063412	0.85[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs10752946	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10752957	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798005	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11484605	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12076560	0.86[ASN][1000 genomes]
rs13932	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs2269613	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2269614	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2269615	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs2269616	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2285170	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs2285171	0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[ASN][1000 genomes]
rs2285172	0.82[ASN][1000 genomes]
rs2285173	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs2285174	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2285175	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2285176	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2301455	0.85[CEU][hapmap];0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2422141	0.99[ASN][1000 genomes]
rs3213563	0.84[ASN][1000 genomes]
rs3937046	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs4916186	0.96[ASN][1000 genomes]
rs4916258	0.84[ASN][1000 genomes]
rs60302909	0.82[ASN][1000 genomes]
rs6424923	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs6658843	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6673869	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs6674073	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs6689377	0.82[ASN][1000 genomes]
rs7411767	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7516301	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs929098	0.82[ASN][1000 genomes]
rs9425308	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9425311	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9425313	0.93[ASN][1000 genomes]
rs9425316	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425598	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9425600	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9425601	0.93[ASN][1000 genomes]
rs9425602	0.93[ASN][1000 genomes]
rs9425604	0.93[ASN][1000 genomes]
rs9425606	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6702667	SNORD79	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172373000-172411800	Weak transcription	Brain Angular Gyrus	brain
2	chr1:172385800-172411000	Weak transcription	Fetal Stomach	stomach
3	chr1:172391000-172410600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:172391000-172412200	Weak transcription	HSMMtube	muscle
5	chr1:172391400-172400800	Weak transcription	Pancreas	Pancrea
6	chr1:172391400-172409400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:172391800-172411000	Weak transcription	Spleen	Spleen
8	chr1:172392000-172412200	Weak transcription	Right Ventricle	heart
9	chr1:172392200-172411000	Weak transcription	Left Ventricle	heart
10	chr1:172392400-172400800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:172392400-172401000	Weak transcription	Lung	lung
12	chr1:172395600-172412200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:172395800-172400600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:172395800-172400600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:172395800-172400600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:172395800-172401000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:172395800-172402800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr1:172396000-172400800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:172396200-172412000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:172396400-172400600	Weak transcription	K562	blood
21	chr1:172396400-172402800	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr1:172396600-172402200	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr1:172396600-172411000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:172396600-172412400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:172396800-172400600	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr1:172396800-172401000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:172396800-172411600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:172396800-172412200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:172397000-172402600	Weak transcription	GM12878-XiMat	blood
30	chr1:172397000-172410000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:172397000-172411000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:172397200-172400600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:172397200-172400600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:172397200-172400800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:172397200-172401000	Weak transcription	Right Atrium	heart
36	chr1:172397200-172402200	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr1:172397800-172401000	Weak transcription	Fetal Intestine Small	intestine
38	chr1:172398600-172400600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:172398800-172401600	Enhancers	Fetal Thymus	thymus
40	chr1:172398800-172402200	Enhancers	Primary T cells fromperipheralblood	blood
41	chr1:172398800-172411000	Weak transcription	Aorta	Aorta
42	chr1:172399000-172400600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:172399000-172400600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:172399000-172407600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr1:172399000-172411600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:172399200-172400800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:172399200-172410800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:172399400-172407000	Weak transcription	Fetal Brain Female	brain
49	chr1:172399600-172401000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:172399800-172401200	Enhancers	Thymus	Thymus

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