Variant report

Variant	rs16962977
Chromosome Location	chr18:29867504-29867505
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	chr18:29867305..29869453-chr18:30048858..30050694,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141441	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10502593	1.00[CEU][hapmap]
rs10502597	1.00[CEU][hapmap]
rs10502598	1.00[CEU][hapmap]
rs10502599	1.00[CEU][hapmap]
rs11660076	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11661174	1.00[EUR][1000 genomes]
rs11661186	0.93[EUR][1000 genomes]
rs11661378	1.00[CEU][hapmap]
rs11664951	1.00[CEU][hapmap]
rs11665544	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11873828	1.00[CEU][hapmap]
rs11877881	1.00[CEU][hapmap]
rs12052010	1.00[CEU][hapmap]
rs1380086	1.00[CEU][hapmap]
rs16962918	0.96[EUR][1000 genomes]
rs16962924	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16962941	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16962953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16962965	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16962971	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16962974	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16963129	1.00[CEU][hapmap]
rs16963184	1.00[CEU][hapmap]
rs17743799	1.00[CEU][hapmap]
rs17743907	1.00[CEU][hapmap]
rs17744164	1.00[CEU][hapmap]
rs17805881	1.00[CEU][hapmap]
rs17805905	1.00[CEU][hapmap]
rs17805953	1.00[CEU][hapmap]
rs17811420	1.00[CEU][hapmap]
rs17811474	1.00[CEU][hapmap]
rs17811780	1.00[CEU][hapmap]
rs28482447	1.00[EUR][1000 genomes]
rs3859366	0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4121653	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs41535045	1.00[CEU][hapmap]
rs4462681	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs60291556	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60694040	0.82[EUR][1000 genomes]
rs7243861	0.93[EUR][1000 genomes]
rs7243963	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs73419859	0.96[EUR][1000 genomes]
rs8086611	1.00[EUR][1000 genomes]
rs8086990	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs8087394	0.96[EUR][1000 genomes]
rs9916917	0.93[EUR][1000 genomes]
rs9947150	1.00[EUR][1000 genomes]
rs9950965	0.90[EUR][1000 genomes]
rs9953127	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9960751	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9962307	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv833616	chr18:29792336-29964212	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv528846	chr18:29832147-29890042	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29839800-29871800	Weak transcription	HSMMtube	muscle
2	chr18:29850000-29877600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr18:29858600-29877600	Weak transcription	Fetal Kidney	kidney
4	chr18:29859000-29867600	Weak transcription	Colonic Mucosa	Colon
5	chr18:29859000-29870400	Weak transcription	HepG2	liver
6	chr18:29861000-29871000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr18:29861000-29876000	Weak transcription	Small Intestine	intestine
8	chr18:29861600-29869400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr18:29861600-29869800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr18:29861600-29876800	Weak transcription	Stomach Mucosa	stomach
11	chr18:29862400-29872400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr18:29862600-29867600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr18:29863000-29869200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr18:29863200-29873000	Weak transcription	Right Ventricle	heart
15	chr18:29863200-29877000	Weak transcription	Fetal Heart	heart
16	chr18:29864000-29868200	Weak transcription	Psoas Muscle	Psoas
17	chr18:29864400-29869400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr18:29864400-29869800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr18:29864400-29870400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr18:29864400-29880800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr18:29864600-29881200	Weak transcription	Colon Smooth Muscle	Colon
22	chr18:29865000-29868000	Strong transcription	Fetal Intestine Small	intestine
23	chr18:29865000-29868000	Strong transcription	Fetal Stomach	stomach
24	chr18:29865000-29868000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr18:29865200-29868000	Strong transcription	Liver	Liver
26	chr18:29865200-29868000	Strong transcription	Brain Hippocampus Middle	brain
27	chr18:29865200-29868200	Strong transcription	Stomach Smooth Muscle	stomach
28	chr18:29865400-29867800	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr18:29865400-29867800	Strong transcription	Pancreas	Pancrea
30	chr18:29865400-29868000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr18:29865400-29868600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr18:29865600-29873200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr18:29865800-29868200	Strong transcription	Fetal Intestine Large	intestine
34	chr18:29865800-29868200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr18:29866200-29868000	Strong transcription	Ovary	ovary
36	chr18:29866200-29869200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr18:29866400-29868200	Strong transcription	Fetal Muscle Leg	muscle
38	chr18:29866600-29867800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr18:29866600-29867800	Strong transcription	Fetal Lung	lung
40	chr18:29866600-29868000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr18:29866600-29868000	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr18:29866600-29868000	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr18:29866600-29868000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr18:29866600-29868000	Strong transcription	Fetal Brain Female	brain
45	chr18:29866600-29868200	Strong transcription	Brain Cingulate Gyrus	brain
46	chr18:29866800-29867800	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr18:29866800-29868000	Strong transcription	Adipose Nuclei	Adipose
48	chr18:29866800-29868000	Strong transcription	Brain Substantia Nigra	brain
49	chr18:29866800-29868000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr18:29866800-29868200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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