Variant report

Variant	rs11929258
Chromosome Location	chr3:160097795-160097796
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:160097729-160097934	K562	blood:	n/a	n/a
2	CEBPB	chr3:160097727-160097938	A549	lung:	n/a	n/a
3	MYC	chr3:160097719-160097900	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr3:160097699-160097868	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr3:160097706-160097897	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr3:160097710-160098042	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160093951..160095466-chr3:160097578..160100383,2	K562	blood:
2	chr3:160093908..160095466-chr3:160097578..160100691,3	K562	blood:
3	chr3:160089762..160091914-chr3:160096661..160098564,2	K562	blood:

Variant related genes	Relation type
IFT80	TF binding region
ENSG00000068885	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12106837	1.00[EUR][1000 genomes]
rs12107576	1.00[EUR][1000 genomes]
rs16831149	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2275150	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2278848	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305402	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs3773370	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56804721	1.00[EUR][1000 genomes]
rs58993492	1.00[EUR][1000 genomes]
rs59308952	1.00[EUR][1000 genomes]
rs6441309	1.00[EUR][1000 genomes]
rs6441310	1.00[EUR][1000 genomes]
rs6764227	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6773833	1.00[EUR][1000 genomes]
rs6773856	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[EUR][1000 genomes]
rs6793718	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs6802789	1.00[EUR][1000 genomes]
rs6808628	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs7614513	1.00[CHB][hapmap]
rs7635305	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160055200-160103400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:160056400-160098000	Weak transcription	Aorta	Aorta
3	chr3:160061400-160109600	Weak transcription	Fetal Heart	heart
4	chr3:160066400-160099200	Weak transcription	NHEK	skin
5	chr3:160067800-160097800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:160069000-160115200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:160071400-160098200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:160071400-160102000	Weak transcription	Small Intestine	intestine
9	chr3:160071600-160099400	Weak transcription	Placenta	Placenta
10	chr3:160073400-160099200	Weak transcription	HSMMtube	muscle
11	chr3:160073800-160108400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:160074800-160101400	Weak transcription	Brain Angular Gyrus	brain
13	chr3:160076200-160116200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:160077400-160098200	Weak transcription	Lung	lung
15	chr3:160081200-160102200	Weak transcription	HUVEC	blood vessel
16	chr3:160081800-160100000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:160083400-160113000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:160083600-160098000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:160083800-160108200	Weak transcription	GM12878-XiMat	blood
20	chr3:160083800-160116000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:160084000-160104000	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:160087600-160098000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:160088200-160099800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:160088800-160101400	Weak transcription	Hela-S3	cervix
25	chr3:160088800-160108600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:160088800-160108600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:160088800-160116200	Weak transcription	Primary B cells from cord blood	blood
28	chr3:160088800-160116200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:160089000-160098000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:160089000-160104000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr3:160091600-160105800	Weak transcription	Ovary	ovary
32	chr3:160092000-160113200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:160092200-160097800	Weak transcription	Thymus	Thymus
34	chr3:160092200-160098200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:160092200-160100400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:160092200-160103200	Weak transcription	K562	blood
37	chr3:160092200-160116000	Weak transcription	Fetal Stomach	stomach
38	chr3:160092200-160116200	Weak transcription	Fetal Intestine Small	intestine
39	chr3:160092200-160116600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:160092400-160097800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:160092600-160097800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:160093000-160102800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:160093000-160113000	Weak transcription	NHLF	lung
44	chr3:160093200-160099400	Weak transcription	Liver	Liver
45	chr3:160093200-160113200	Weak transcription	Brain Germinal Matrix	brain
46	chr3:160093400-160100800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:160093600-160116000	Weak transcription	Fetal Kidney	kidney
48	chr3:160094000-160100000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr3:160094200-160097800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:160094400-160100200	Weak transcription	Adipose Nuclei	Adipose

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