Variant report

Variant	rs9962307
Chromosome Location	chr18:29854892-29854893
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29847813..29851392-chr18:29854747..29858581,3	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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];0.85[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];0.85[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]
rs16962941	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16962953	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MKK][hapmap];0.96[EUR][1000 genomes]
rs16962965	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16962971	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962974	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16962977	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]
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	1.00[GIH][hapmap];0.93[MKK][hapmap];0.96[EUR][1000 genomes]
rs41535045	1.00[CEU][hapmap]
rs4462681	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][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	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8086990	1.00[CEU][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8087394	0.96[EUR][1000 genomes]
rs8097937	1.00[MEX][hapmap]
rs9916917	0.93[EUR][1000 genomes]
rs9947150	1.00[EUR][1000 genomes]
rs9950965	0.90[EUR][1000 genomes]
rs9953127	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9960751	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9962307	DSG2	cis	lymphoblastoid	seeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29835200-29861600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:29837400-29867200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:29839800-29871800	Weak transcription	HSMMtube	muscle
4	chr18:29843000-29867000	Weak transcription	Brain Angular Gyrus	brain
5	chr18:29845200-29857400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr18:29846000-29867000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr18:29847000-29856600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr18:29848200-29863600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr18:29848400-29860200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:29848600-29857400	Weak transcription	HepG2	liver
11	chr18:29848600-29867200	Weak transcription	Lung	lung
12	chr18:29848800-29866600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr18:29849400-29856800	Weak transcription	Right Ventricle	heart
14	chr18:29849400-29867000	Weak transcription	Esophagus	oesophagus
15	chr18:29849800-29857400	Weak transcription	Brain Anterior Caudate	brain
16	chr18:29849800-29867000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr18:29850000-29857000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr18:29850000-29860600	Weak transcription	Brain Substantia Nigra	brain
19	chr18:29850000-29877600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr18:29850200-29856200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr18:29850200-29856800	Weak transcription	Brain Hippocampus Middle	brain
22	chr18:29850200-29857000	Weak transcription	Adipose Nuclei	Adipose
23	chr18:29850200-29857400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr18:29850200-29858400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr18:29850200-29866600	Weak transcription	Fetal Lung	lung
26	chr18:29850200-29867000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr18:29850200-29867000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr18:29850400-29855200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr18:29850400-29857000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr18:29850400-29858200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr18:29850400-29858800	Weak transcription	Ovary	ovary
32	chr18:29850400-29860200	Weak transcription	Left Ventricle	heart
33	chr18:29850400-29865800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr18:29850400-29866600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr18:29850400-29867200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr18:29850600-29856800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr18:29850600-29856800	Weak transcription	Pancreas	Pancrea
38	chr18:29850600-29858800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr18:29850600-29860400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr18:29850600-29860600	Weak transcription	Fetal Muscle Leg	muscle
41	chr18:29852200-29855000	Weak transcription	Fetal Intestine Small	intestine
42	chr18:29852200-29855200	Weak transcription	Fetal Intestine Large	intestine
43	chr18:29852200-29856000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr18:29852200-29856000	Weak transcription	Fetal Kidney	kidney
45	chr18:29852200-29856800	Weak transcription	Aorta	Aorta
46	chr18:29852200-29856800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr18:29852200-29857200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr18:29852200-29857400	Weak transcription	Liver	Liver
49	chr18:29852200-29865000	Weak transcription	Fetal Stomach	stomach
50	chr18:29852400-29856000	Weak transcription	Colonic Mucosa	Colon

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