Variant report

Variant	rs16962941
Chromosome Location	chr18:29845289-29845290
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	chr18:29843865..29846147-chr18:30049369..30051018,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141441	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

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];0.92[AMR][1000 genomes];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];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];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]
rs16962953	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16962965	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16962971	1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962974	1.00[CEU][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962977	1.00[CEU][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	0.96[EUR][1000 genomes]
rs41535045	1.00[CEU][hapmap]
rs4462681	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs60291556	0.96[EUR][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	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8086990	1.00[CEU][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8087394	0.91[AFR][1000 genomes];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];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9960751	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9962307	1.00[CEU][hapmap];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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29823800-29848000	Weak transcription	Aorta	Aorta
2	chr18:29831400-29847600	Weak transcription	Pancreas	Pancrea
3	chr18:29835200-29861600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr18:29837400-29847800	Weak transcription	Right Ventricle	heart
5	chr18:29837400-29867200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:29837600-29848200	Weak transcription	Colonic Mucosa	Colon
7	chr18:29838000-29847600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr18:29838000-29848000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr18:29838400-29847600	Weak transcription	Brain Hippocampus Middle	brain
10	chr18:29838600-29848000	Weak transcription	HepG2	liver
11	chr18:29838600-29851400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr18:29838600-29851600	Weak transcription	Stomach Mucosa	stomach
13	chr18:29838800-29846800	Weak transcription	Liver	Liver
14	chr18:29838800-29846800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr18:29839000-29847600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr18:29839000-29847800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr18:29839200-29847600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr18:29839800-29871800	Weak transcription	HSMMtube	muscle
19	chr18:29840000-29847800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr18:29841000-29847800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr18:29842600-29847600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr18:29842800-29848000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr18:29843000-29867000	Weak transcription	Brain Angular Gyrus	brain
24	chr18:29843200-29845400	Weak transcription	Adipose Nuclei	Adipose
25	chr18:29843200-29847800	Weak transcription	Fetal Muscle Leg	muscle
26	chr18:29843400-29847600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr18:29843400-29847800	Weak transcription	Brain Anterior Caudate	brain
28	chr18:29843400-29848000	Weak transcription	Ovary	ovary
29	chr18:29843600-29847600	Weak transcription	Brain Substantia Nigra	brain
30	chr18:29844000-29847600	Weak transcription	Gastric	stomach
31	chr18:29844200-29847400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr18:29844200-29848600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr18:29844400-29847000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr18:29844600-29846200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr18:29844800-29847600	Weak transcription	Fetal Kidney	kidney
36	chr18:29844800-29848200	Weak transcription	Fetal Brain Female	brain
37	chr18:29845000-29847400	Weak transcription	Fetal Lung	lung
38	chr18:29845000-29848000	Weak transcription	Fetal Intestine Small	intestine
39	chr18:29845200-29846800	Weak transcription	Fetal Intestine Large	intestine
40	chr18:29845200-29852000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr18:29845200-29857400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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