Variant report

Variant	rs4791227
Chromosome Location	chr17:63178272-63178273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:63178028..63180075-chr17:63181062..63183673,2	K562	blood:
2	chr17:63117639..63119496-chr17:63177929..63179773,2	MCF-7	breast:
3	chr17:63173795..63175589-chr17:63177989..63180729,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265883	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10514867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11650746	0.94[ASN][1000 genomes]
rs11651062	0.94[ASN][1000 genomes]
rs11651081	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654243	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654391	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11657250	0.94[ASN][1000 genomes]
rs11658655	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11658673	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658736	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658773	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1514500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16960903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960957	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961015	1.00[CHB][hapmap]
rs16961273	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28451574	0.81[ASN][1000 genomes]
rs28525077	0.81[ASN][1000 genomes]
rs2869578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869579	0.94[ASN][1000 genomes]
rs2869580	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2869582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2869584	0.94[ASN][1000 genomes]
rs4293415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4588019	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4791220	0.88[CEU][hapmap]
rs4791223	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791228	0.81[EUR][1000 genomes]
rs55948632	0.81[ASN][1000 genomes]
rs55948933	0.94[ASN][1000 genomes]
rs56102951	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59173947	0.81[ASN][1000 genomes]
rs61708414	0.81[ASN][1000 genomes]
rs7207726	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs7211341	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215502	0.94[ASN][1000 genomes]
rs7217524	1.00[JPT][hapmap]
rs7217548	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7218518	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7220710	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7220949	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7221103	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73330407	0.87[ASN][1000 genomes]
rs73347632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8065444	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8065725	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8066063	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8066072	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8068016	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8071603	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8072543	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8080929	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs908089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9889653	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9896245	0.81[ASW][hapmap];1.00[CEU][hapmap]
rs9897592	1.00[CEU][hapmap]
rs9898825	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9900568	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9900709	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9901108	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9904207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9907146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9907374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9908359	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9914418	0.94[ASN][1000 genomes]
rs9914790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9916092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9916789	0.94[ASN][1000 genomes]

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	nsv530764	chr17:62939944-63278472	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4791227	TBX2	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:63157000-63179800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:63160000-63180400	Weak transcription	Brain Substantia Nigra	brain
3	chr17:63169800-63190800	Weak transcription	Gastric	stomach
4	chr17:63170000-63178400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr17:63170000-63180200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:63173000-63179800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr17:63173400-63179800	Weak transcription	Aorta	Aorta
8	chr17:63173600-63180000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:63174400-63179800	Weak transcription	NH-A	brain
10	chr17:63174400-63180000	Weak transcription	Osteobl	bone
11	chr17:63175000-63179000	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr17:63175000-63179200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr17:63175000-63179200	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr17:63175000-63179400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:63175200-63178800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr17:63175200-63179000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr17:63175400-63178400	Weak transcription	Placenta	Placenta
18	chr17:63175400-63179600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr17:63175400-63179800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr17:63175400-63179800	Weak transcription	Brain Hippocampus Middle	brain
21	chr17:63176000-63178400	Weak transcription	HUVEC	blood vessel
22	chr17:63176000-63179600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr17:63176000-63180000	Weak transcription	NHLF	lung
24	chr17:63176000-63181000	Weak transcription	Fetal Kidney	kidney
25	chr17:63176200-63178400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr17:63176200-63178800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:63176200-63179600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:63176200-63179600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:63176200-63179800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:63176200-63179800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:63176200-63180400	Weak transcription	Brain Angular Gyrus	brain
32	chr17:63176200-63180400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr17:63176400-63178600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr17:63176400-63179000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr17:63176400-63179200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr17:63176400-63179600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr17:63176400-63179600	Weak transcription	Fetal Brain Male	brain
38	chr17:63176400-63179800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr17:63176400-63179800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr17:63176400-63179800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr17:63176400-63179800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr17:63176400-63180000	Weak transcription	Brain Anterior Caudate	brain
43	chr17:63176400-63223800	Weak transcription	Lung	lung
44	chr17:63176600-63178400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr17:63176600-63179600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:63176600-63180600	Enhancers	Primary T cells fromperipheralblood	blood
47	chr17:63176800-63179200	Enhancers	Dnd41	blood
48	chr17:63177200-63179000	Enhancers	Primary B cells from peripheral blood	blood
49	chr17:63177200-63179000	Enhancers	Fetal Thymus	thymus
50	chr17:63177400-63178600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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