Variant report

Variant	rs17767294
Chromosome Location	chr6:28054198-28054199
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28054146..28055764-chr6:28072126..28074128,2	K562	blood:
2	chr6:28047399..28050542-chr6:28051923..28057231,4	MCF-7	breast:
3	chr6:28047374..28049221-chr6:28051940..28054259,3	MCF-7	breast:
4	chr6:28053376..28055027-chr6:28058421..28061331,2	K562	blood:
5	chr6:28047913..28051449-chr6:28052832..28058819,8	K562	blood:
6	chr6:28053744..28056294-chr6:28058475..28060546,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000219891	Chromatin interaction
ENSG00000197279	Chromatin interaction
ENSG00000272009	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10046419	1.00[CHB][hapmap]
rs12332927	0.82[CHB][hapmap]
rs1497525	1.00[CHB][hapmap]
rs1497526	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs1564442	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.93[YRI][hapmap];0.94[ASN][1000 genomes]
rs16893533	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs16893540	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs16893638	0.94[ASN][1000 genomes]
rs16893731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[ASN][1000 genomes]
rs16893761	0.94[ASN][1000 genomes]
rs16893801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs16893827	0.82[JPT][hapmap]
rs17720687	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs17765402	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1873213	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs2277103	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.93[YRI][hapmap];0.94[ASN][1000 genomes]
rs2299030	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs35027728	0.94[ASN][1000 genomes]
rs3757186	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];0.94[ASN][1000 genomes]
rs59910759	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6456803	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs6900413	0.82[CHB][hapmap]
rs73396575	0.94[ASN][1000 genomes]
rs73400515	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73400532	0.94[ASN][1000 genomes]
rs73400551	0.94[ASN][1000 genomes]
rs7757215	0.82[JPT][hapmap]
rs7760871	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs9461424	1.00[CHB][hapmap]
rs9461425	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs9468252	0.82[CHB][hapmap]
rs9468254	1.00[CHB][hapmap]
rs9468264	1.00[CHB][hapmap]
rs9885649	0.82[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17767294	OR1F12	cis	Thyroid	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28049400-28055400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:28049400-28056600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:28049400-28056800	Weak transcription	Aorta	Aorta
4	chr6:28049600-28054200	Weak transcription	Thymus	Thymus
5	chr6:28049600-28054800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:28049600-28055000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:28049600-28055200	Weak transcription	Colonic Mucosa	Colon
8	chr6:28049600-28055400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:28049600-28055600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:28049600-28055600	Weak transcription	Fetal Kidney	kidney
11	chr6:28049600-28056000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr6:28049600-28056000	Weak transcription	Left Ventricle	heart
13	chr6:28049600-28056400	Weak transcription	Esophagus	oesophagus
14	chr6:28049600-28056400	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:28049600-28056600	Weak transcription	Psoas Muscle	Psoas
16	chr6:28049600-28057000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:28049600-28058600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:28049600-28058600	Weak transcription	Brain Substantia Nigra	brain
19	chr6:28049600-28059200	Weak transcription	Fetal Brain Male	brain
20	chr6:28049600-28063000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:28049800-28055400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:28049800-28055400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:28049800-28055400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:28049800-28055400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:28049800-28055600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:28049800-28055600	Weak transcription	Stomach Mucosa	stomach
27	chr6:28049800-28056000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:28049800-28056200	Weak transcription	Adipose Nuclei	Adipose
29	chr6:28049800-28056800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:28049800-28056800	Weak transcription	HSMMtube	muscle
31	chr6:28049800-28057000	Weak transcription	Fetal Heart	heart
32	chr6:28049800-28057600	Weak transcription	Brain Hippocampus Middle	brain
33	chr6:28049800-28058600	Weak transcription	Brain Germinal Matrix	brain
34	chr6:28049800-28058600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:28050000-28055400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr6:28050000-28055800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:28050000-28056800	Weak transcription	Brain Anterior Caudate	brain
38	chr6:28050800-28061200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:28051200-28058600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:28051600-28056000	Weak transcription	K562	blood
41	chr6:28051800-28055400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:28052000-28055600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:28052800-28055600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr6:28053200-28054200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr6:28053200-28054600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:28053200-28054600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:28053200-28054800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:28053200-28054800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr6:28053200-28054800	Strong transcription	HMEC	breast
50	chr6:28053200-28055200	Strong transcription	H1 Cell Line	embryonic stem cell

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