Variant report

Variant	rs2929385
Chromosome Location	chr3:19931170-19931171
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:19930446..19931966-chr3:19932163..19933731,2	MCF-7	breast:
2	chr3:19930434..19932349-chr3:19933276..19934867,2	K562	blood:
3	chr3:19930617..19933383-chr3:19987388..19990668,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2171275	0.81[GIH][hapmap];0.84[MEX][hapmap]
rs2931394	0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1003183	chr3:19671647-19948351	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2929385	DPH3	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19927400-19941200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:19929600-19931800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr3:19930000-19931200	Enhancers	HMEC	breast
4	chr3:19930000-19931400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:19930000-19931400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:19930000-19931600	Enhancers	Fetal Intestine Small	intestine
7	chr3:19930000-19931600	Enhancers	HSMM	muscle
8	chr3:19930000-19932000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:19930000-19932800	Enhancers	Fetal Stomach	stomach
10	chr3:19930200-19931400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:19930200-19931400	Enhancers	Fetal Intestine Large	intestine
12	chr3:19930200-19931400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
13	chr3:19930200-19931400	Active TSS	Right Atrium	heart
14	chr3:19930400-19931200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:19930400-19931200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:19930400-19931200	Flanking Active TSS	Hela-S3	cervix
17	chr3:19930400-19931200	Flanking Active TSS	NHEK	skin
18	chr3:19930400-19931400	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr3:19930400-19931400	Weak transcription	Small Intestine	intestine
20	chr3:19930400-19931600	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr3:19930400-19931600	Enhancers	Fetal Muscle Leg	muscle
22	chr3:19930400-19931800	Active TSS	Brain Anterior Caudate	brain
23	chr3:19930600-19931200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:19930600-19931200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:19930600-19931200	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr3:19930600-19931200	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr3:19930600-19931200	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr3:19930600-19931200	Active TSS	A549	lung
29	chr3:19930600-19931400	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr3:19930600-19931800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:19930600-19932400	Enhancers	Placenta	Placenta
32	chr3:19930600-19933200	Weak transcription	Gastric	stomach
33	chr3:19930800-19931200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:19930800-19931200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:19930800-19931200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:19930800-19931200	Active TSS	Brain Hippocampus Middle	brain
37	chr3:19930800-19931200	Active TSS	Colon Smooth Muscle	Colon
38	chr3:19930800-19931400	Active TSS	Brain Angular Gyrus	brain
39	chr3:19930800-19931400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:19930800-19931400	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr3:19930800-19931400	Enhancers	NH-A	brain
42	chr3:19930800-19931400	Active TSS	NHDF-Ad	bronchial
43	chr3:19930800-19931400	Active TSS	NHLF	lung
44	chr3:19930800-19931600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:19930800-19931800	Active TSS	Brain Cingulate Gyrus	brain
46	chr3:19930800-19931800	Active TSS	Brain Substantia Nigra	brain
47	chr3:19930800-19931800	Enhancers	HUVEC	blood vessel
48	chr3:19931000-19931200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:19931000-19931200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr3:19931000-19931200	Active TSS	Ovary	ovary

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