Variant report

Variant	rs229664
Chromosome Location	chr14:65171577-65171578
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:64968210..64972351-chr14:65168934..65172584,5	MCF-7	breast:
2	chr12:98987199..98987981-chr14:65171448..65172373,2	Hela-S3	cervix:
3	chr14:65168373..65176902-chr14:65220182..65231670,21	MCF-7	breast:
4	chr14:65168529..65178400-chr14:65179583..65195815,52	MCF-7	breast:
5	chr14:65171254..65174488-chr14:65196605..65199995,3	MCF-7	breast:
6	chr14:65170433..65175465-chr14:65207632..65214317,8	MCF-7	breast:
7	chr14:65168335..65178043-chr14:65220677..65234710,31	MCF-7	breast:
8	chr14:64968319..64971699-chr14:65168654..65172546,5	MCF-7	breast:
9	chr14:65170634..65173219-chr14:65206307..65208864,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000070182	Chromatin interaction
ENSG00000126804	Chromatin interaction
ENSG00000075415	Chromatin interaction
ENSG00000089775	Chromatin interaction
ENSG00000126822	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs17179970	0.95[ASN][1000 genomes]
rs17179984	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17180090	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs17767188	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs17767206	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[ASN][1000 genomes]
rs1985465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1985466	0.87[ASN][1000 genomes]
rs1998120	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs229603	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs229620	0.87[ASN][1000 genomes]
rs229624	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs229625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs229626	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs229644	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs229646	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs229650	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs229651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs229655	0.87[ASN][1000 genomes]
rs229659	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs229660	1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs229662	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229663	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229665	0.88[EUR][1000 genomes]
rs41301473	1.00[ASN][1000 genomes]
rs41307086	0.95[ASN][1000 genomes]
rs58789159	1.00[ASN][1000 genomes]
rs73273513	0.87[ASN][1000 genomes]
rs73273517	0.91[ASN][1000 genomes]
rs73273524	1.00[ASN][1000 genomes]
rs73273534	1.00[ASN][1000 genomes]
rs73273536	1.00[ASN][1000 genomes]
rs73273546	0.91[ASN][1000 genomes]
rs73273549	1.00[ASN][1000 genomes]
rs754435	1.00[ASN][1000 genomes]
rs872296	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049097	chr14:65027753-65202018	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3437023	chr14:65170024-65173072	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs229664	SIX1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65169200-65172600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr14:65169400-65172600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr14:65169600-65172200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:65169800-65172200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr14:65169800-65172200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr14:65169800-65172400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr14:65169800-65172600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
8	chr14:65169800-65173600	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr14:65170000-65172600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr14:65170000-65176600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr14:65170200-65172200	Active TSS	Small Intestine	intestine
12	chr14:65170200-65172600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr14:65170400-65172400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr14:65170400-65172400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr14:65170400-65172600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr14:65170400-65172800	Active TSS	Brain Cingulate Gyrus	brain
17	chr14:65170600-65171600	Flanking Bivalent TSS/Enh	Thymus	Thymus
18	chr14:65170600-65172000	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr14:65170600-65172200	Active TSS	Esophagus	oesophagus
20	chr14:65170600-65172400	Active TSS	Fetal Kidney	kidney
21	chr14:65170600-65172400	Active TSS	Ovary	ovary
22	chr14:65170600-65172600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr14:65170600-65172800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr14:65170600-65172800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr14:65170600-65173200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr14:65170600-65173400	Active TSS	Aorta	Aorta
27	chr14:65170800-65171600	Bivalent/Poised TSS	Primary T helper naive cells from peripheral blood	blood
28	chr14:65170800-65171600	Bivalent/Poised TSS	Fetal Brain Female	brain
29	chr14:65170800-65171800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr14:65170800-65171800	Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr14:65170800-65171800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
32	chr14:65170800-65171800	Active TSS	Fetal Lung	lung
33	chr14:65170800-65171800	Active TSS	Placenta	Placenta
34	chr14:65170800-65172000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr14:65170800-65172000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr14:65170800-65172000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr14:65170800-65172000	Active TSS	Stomach Mucosa	stomach
38	chr14:65170800-65172000	Bivalent/Poised TSS	HepG2	liver
39	chr14:65170800-65172200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr14:65170800-65172200	Active TSS	A549	lung
41	chr14:65170800-65172200	Active TSS	HSMMtube	muscle
42	chr14:65170800-65172400	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr14:65170800-65172400	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr14:65170800-65172400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr14:65170800-65172400	Active TSS	Placenta Amnion	Placenta Amnion
46	chr14:65170800-65172400	Active TSS	Rectal Smooth Muscle	rectum
47	chr14:65170800-65172400	Active TSS	NHDF-Ad	bronchial
48	chr14:65170800-65172600	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr14:65170800-65172600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr14:65170800-65172600	Active TSS	Brain Hippocampus Middle	brain

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