Variant report

Variant	rs4799626
Chromosome Location	chr18:29605094-29605095
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	chr18:29598566..29600531-chr18:29604153..29606634,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263917	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12455890	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12458564	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2162379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4799624	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7226474	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7236547	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065285	chr18:29527884-29614986	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv1803283	chr18:29591102-29640430	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4799626	DSG2	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29599600-29629600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr18:29600200-29617200	Weak transcription	Lung	lung
3	chr18:29600400-29605800	Weak transcription	Primary B cells from cord blood	blood
4	chr18:29600400-29606200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr18:29600400-29616800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr18:29600400-29617000	Weak transcription	Fetal Muscle Leg	muscle
7	chr18:29600600-29605600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr18:29600600-29605600	Weak transcription	GM12878-XiMat	blood
9	chr18:29600600-29616800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr18:29600600-29617000	Weak transcription	Left Ventricle	heart
11	chr18:29600600-29620400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr18:29600600-29628400	Weak transcription	Hela-S3	cervix
13	chr18:29600800-29605400	Weak transcription	Thymus	Thymus
14	chr18:29600800-29632400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr18:29601000-29605200	Weak transcription	Fetal Thymus	thymus
16	chr18:29601000-29606800	Weak transcription	Psoas Muscle	Psoas
17	chr18:29601600-29605400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr18:29602000-29617200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr18:29602200-29607200	Genic enhancers	Primary T cells fromperipheralblood	blood
20	chr18:29602400-29605600	Weak transcription	Adipose Nuclei	Adipose
21	chr18:29602400-29611000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr18:29602600-29605200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr18:29602600-29606400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr18:29602600-29606400	Weak transcription	Brain Anterior Caudate	brain
25	chr18:29602600-29610400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr18:29602600-29610400	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr18:29602600-29617000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr18:29602600-29628600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr18:29602600-29664200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr18:29602800-29605800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr18:29602800-29606600	Weak transcription	Brain Substantia Nigra	brain
32	chr18:29602800-29616600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr18:29602800-29617000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr18:29602800-29617200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr18:29602800-29617200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr18:29602800-29617400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr18:29602800-29620600	Weak transcription	Brain Angular Gyrus	brain
38	chr18:29603000-29606000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr18:29603200-29605200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr18:29603200-29608800	Weak transcription	Small Intestine	intestine
41	chr18:29603400-29605600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr18:29603400-29605600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
43	chr18:29603600-29605200	Weak transcription	Brain Hippocampus Middle	brain
44	chr18:29603600-29617200	Weak transcription	Fetal Intestine Large	intestine
45	chr18:29603800-29605200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr18:29603800-29605200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr18:29603800-29610800	Weak transcription	Liver	Liver
48	chr18:29604000-29605800	Weak transcription	Primary T cells from cord blood	blood
49	chr18:29604200-29610400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr18:29604400-29606400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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