Variant report

Variant	rs11708118
Chromosome Location	chr3:160110255-160110256
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160107096..160111535-chr3:160116072..160118886,5	K562	blood:
2	chr3:160103919..160105647-chr3:160110013..160112300,2	K562	blood:
3	chr3:160108609..160112041-chr3:160112048..160115304,5	K562	blood:
4	chr3:160109714..160114340-chr3:160115378..160118929,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113810	Chromatin interaction
ENSG00000068885	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1047210	0.82[JPT][hapmap]
rs10923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10936201	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10936203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11706810	0.82[JPT][hapmap]
rs11709232	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11716413	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11719750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11720689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12152435	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12630564	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12630770	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12630956	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12632030	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12638633	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12639488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs16831207	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236494	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17826137	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17826173	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17826221	0.82[JPT][hapmap]
rs17826257	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs1873076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2095529	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2099496	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2275151	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3773369	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4679886	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679892	0.83[EUR][1000 genomes]
rs4680581	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680586	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56952700	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60395700	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441311	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6798183	0.82[JPT][hapmap]
rs6809153	0.82[JPT][hapmap]
rs73875254	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73875259	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73875285	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73875290	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7620828	0.82[JPT][hapmap]
rs7627555	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
8	esv1795255	chr3:160089896-160153305	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	205 gene(s)	inside rSNPs	diseases
9	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11708118	IFT80	cis	cerebellum	SCAN
rs11708118	SMC4	Cis_1M	lymphoblastoid	RTeQTL
rs11708118	IFT80	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160069000-160115200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:160076200-160116200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:160083400-160113000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:160083800-160116000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:160088800-160116200	Weak transcription	Primary B cells from cord blood	blood
6	chr3:160088800-160116200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:160092000-160113200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:160092200-160116000	Weak transcription	Fetal Stomach	stomach
9	chr3:160092200-160116200	Weak transcription	Fetal Intestine Small	intestine
10	chr3:160092200-160116600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:160093000-160113000	Weak transcription	NHLF	lung
12	chr3:160093200-160113200	Weak transcription	Brain Germinal Matrix	brain
13	chr3:160093600-160116000	Weak transcription	Fetal Kidney	kidney
14	chr3:160094600-160116000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:160094800-160113000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:160094800-160113200	Weak transcription	HSMM	muscle
17	chr3:160094800-160115800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:160094800-160116000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:160094800-160116000	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:160094800-160116600	Weak transcription	Left Ventricle	heart
21	chr3:160095000-160115800	Weak transcription	Fetal Intestine Large	intestine
22	chr3:160095000-160116000	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:160095200-160115000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:160095400-160113200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:160095400-160116000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:160097000-160113200	Weak transcription	A549	lung
27	chr3:160098200-160113400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:160098400-160113400	Weak transcription	Dnd41	blood
29	chr3:160098400-160115200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:160098400-160116200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:160098400-160116400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:160098800-160115600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr3:160098800-160115800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:160098800-160116200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:160099000-160113200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:160099400-160113200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:160099400-160116000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:160100000-160113000	Weak transcription	Osteobl	bone
39	chr3:160100200-160113000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:160103200-160116000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:160103600-160115400	Weak transcription	Thymus	Thymus
42	chr3:160103600-160116000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:160103800-160113000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:160104600-160111800	Weak transcription	Primary T cells from cord blood	blood
45	chr3:160109000-160115600	Weak transcription	Fetal Thymus	thymus
46	chr3:160109000-160116200	Weak transcription	Stomach Mucosa	stomach
47	chr3:160109200-160113200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:160109200-160113200	Weak transcription	GM12878-XiMat	blood
49	chr3:160109600-160111600	Enhancers	K562	blood
50	chr3:160109600-160112200	Enhancers	Fetal Heart	heart

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