Variant report

Variant	rs16977229
Chromosome Location	chr18:12489938-12489939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12464094..12466231-chr18:12487109..12489946,2	MCF-7	breast:
2	chr18:12488792..12490791-chr18:12657276..12659275,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128789	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000134278	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1019839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1019840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11080579	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12605607	0.88[CHB][hapmap];0.89[JPT][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12607907	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap];0.98[ASN][1000 genomes]
rs12607911	0.88[CHB][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs12607972	0.88[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs16939654	1.00[CHD][hapmap]
rs17524618	0.98[ASN][1000 genomes]
rs17525206	0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs17615418	0.88[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs1978653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34518007	1.00[CHD][hapmap]
rs58964661	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7230926	0.88[CHB][hapmap];0.88[JPT][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7235783	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237432	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv2208	chr18:12472999-12518189	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	esv2756075	chr18:12481377-12548970	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12460200-12516600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr18:12461400-12495400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr18:12463400-12491800	Weak transcription	Psoas Muscle	Psoas
4	chr18:12465000-12491400	Weak transcription	NHDF-Ad	bronchial
5	chr18:12465600-12500800	Weak transcription	Fetal Intestine Large	intestine
6	chr18:12472600-12495200	Weak transcription	Colonic Mucosa	Colon
7	chr18:12477200-12490800	Weak transcription	K562	blood
8	chr18:12478400-12512600	Weak transcription	Fetal Intestine Small	intestine
9	chr18:12478600-12496000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr18:12478600-12498400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr18:12478600-12506400	Weak transcription	Right Ventricle	heart
12	chr18:12478600-12510800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr18:12478800-12490800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr18:12478800-12491200	Weak transcription	Liver	Liver
15	chr18:12478800-12491400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr18:12478800-12491400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr18:12478800-12491400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr18:12478800-12491400	Weak transcription	Brain Anterior Caudate	brain
19	chr18:12478800-12491400	Weak transcription	Fetal Brain Female	brain
20	chr18:12478800-12491400	Weak transcription	Fetal Lung	lung
21	chr18:12478800-12491400	Weak transcription	HepG2	liver
22	chr18:12478800-12491400	Weak transcription	Osteobl	bone
23	chr18:12478800-12491600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr18:12478800-12491600	Weak transcription	Brain Hippocampus Middle	brain
25	chr18:12478800-12491600	Weak transcription	Colon Smooth Muscle	Colon
26	chr18:12478800-12491600	Weak transcription	Esophagus	oesophagus
27	chr18:12478800-12491600	Weak transcription	Fetal Kidney	kidney
28	chr18:12478800-12491600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr18:12478800-12491600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr18:12478800-12491600	Weak transcription	Spleen	Spleen
31	chr18:12478800-12492000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr18:12478800-12492800	Weak transcription	Fetal Brain Male	brain
33	chr18:12478800-12497400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr18:12478800-12499600	Weak transcription	NHLF	lung
35	chr18:12478800-12504800	Weak transcription	Gastric	stomach
36	chr18:12478800-12505800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr18:12478800-12514200	Weak transcription	NH-A	brain
38	chr18:12478800-12515800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr18:12478800-12515800	Weak transcription	Placenta	Placenta
40	chr18:12478800-12551800	Weak transcription	Pancreas	Pancrea
41	chr18:12479000-12491400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr18:12479200-12491600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr18:12479200-12491800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr18:12479600-12491400	Weak transcription	Brain Germinal Matrix	brain
45	chr18:12479800-12491200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr18:12479800-12491400	Weak transcription	Fetal Muscle Leg	muscle
47	chr18:12479800-12491400	Weak transcription	Fetal Stomach	stomach
48	chr18:12479800-12491600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr18:12479800-12491600	Weak transcription	Aorta	Aorta
50	chr18:12479800-12491600	Weak transcription	Lung	lung

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