Variant report

Variant	rs9884030
Chromosome Location	chr3:42628270-42628271
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42622045..42625365-chr3:42627615..42632564,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000093183	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10154957	1.00[AMR][1000 genomes]
rs13320598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13325536	1.00[AMR][1000 genomes]
rs28508060	1.00[AMR][1000 genomes]
rs28549046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs580447	1.00[AMR][1000 genomes]
rs58273990	1.00[AMR][1000 genomes]
rs9812538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9812673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9822273	1.00[AMR][1000 genomes]
rs9832720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9841926	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9853946	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs9855071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9869491	1.00[AMR][1000 genomes]
rs9876937	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs9985232	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42624200-42631400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:42624200-42631600	Weak transcription	HSMMtube	muscle
3	chr3:42624400-42629800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:42624400-42629800	Weak transcription	NHEK	skin
5	chr3:42624400-42631200	Weak transcription	Brain Anterior Caudate	brain
6	chr3:42624400-42631200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:42624400-42631200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:42624400-42631400	Weak transcription	Liver	Liver
9	chr3:42624400-42631400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:42624400-42631400	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:42624400-42632400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:42624600-42631200	Weak transcription	Adipose Nuclei	Adipose
13	chr3:42624600-42631400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:42624600-42631400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:42624600-42631400	Weak transcription	Fetal Brain Male	brain
16	chr3:42624600-42631400	Weak transcription	A549	lung
17	chr3:42624800-42630200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:42624800-42631400	Weak transcription	Primary B cells from cord blood	blood
19	chr3:42624800-42631400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:42624800-42631400	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:42624800-42631400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:42624800-42631400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:42624800-42631600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:42624800-42631600	Weak transcription	Gastric	stomach
25	chr3:42625000-42630200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:42625000-42631000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:42625000-42631000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:42625000-42631200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:42625000-42631200	Weak transcription	GM12878-XiMat	blood
30	chr3:42625000-42631400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:42625000-42631400	Weak transcription	Brain Germinal Matrix	brain
32	chr3:42625000-42631400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:42625000-42631400	Weak transcription	Fetal Intestine Small	intestine
34	chr3:42625000-42631600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:42625200-42631400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:42625200-42631600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:42625400-42631400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:42625400-42631400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:42625600-42631200	Weak transcription	Dnd41	blood
40	chr3:42625600-42631400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:42625600-42631400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:42628000-42631200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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