Variant report

Variant	rs9838780
Chromosome Location	chr3:17331026-17331027
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:17330285..17331951-chr3:17337409..17339614,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs7650336	1.00[AFR][1000 genomes]
rs9631485	0.88[AFR][1000 genomes]
rs9841955	1.00[AFR][1000 genomes]
rs9858820	0.88[AFR][1000 genomes]
rs9864049	1.00[AFR][1000 genomes]
rs9866815	1.00[AFR][1000 genomes]
rs9880199	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876589	chr3:17230884-17346355	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv876590	chr3:17230884-17604963	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2755406	chr3:17237396-17589896	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv876591	chr3:17246392-17671992	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17255200-17363800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:17298800-17373000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:17301400-17335400	Weak transcription	Ovary	ovary
4	chr3:17313800-17332200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:17315000-17332400	Weak transcription	GM12878-XiMat	blood
6	chr3:17319600-17332400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:17319600-17332400	Weak transcription	Adipose Nuclei	Adipose
8	chr3:17319800-17351200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:17320800-17332200	Weak transcription	Colonic Mucosa	Colon
10	chr3:17321200-17332200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:17321600-17332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:17321600-17354200	Weak transcription	Placenta	Placenta
13	chr3:17321800-17332000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:17322200-17342800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:17323000-17334600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:17324600-17333000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:17327400-17333000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr3:17327800-17343000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:17328000-17332400	Weak transcription	Fetal Lung	lung
20	chr3:17328400-17341400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:17328600-17331400	Strong transcription	Primary T cells from cord blood	blood
22	chr3:17328600-17332400	Weak transcription	HepG2	liver
23	chr3:17328800-17334000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:17328800-17334600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:17328800-17343800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:17329000-17331600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:17329000-17332400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:17329000-17333600	Weak transcription	Brain Angular Gyrus	brain
29	chr3:17329000-17334400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:17329000-17336400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:17329000-17340400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:17329000-17342000	Weak transcription	HSMM	muscle
33	chr3:17329000-17344200	Weak transcription	Psoas Muscle	Psoas
34	chr3:17329200-17331200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:17329200-17331600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:17329200-17333800	Strong transcription	Primary B cells from cord blood	blood
37	chr3:17329200-17343000	Weak transcription	Brain Anterior Caudate	brain
38	chr3:17329200-17344400	Weak transcription	Brain Substantia Nigra	brain
39	chr3:17329600-17333400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:17329600-17342000	Weak transcription	Fetal Thymus	thymus
41	chr3:17329800-17331200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:17329800-17333800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:17330000-17333000	Weak transcription	HSMMtube	muscle
44	chr3:17330000-17333600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr3:17330000-17341600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:17330200-17331400	Strong transcription	Fetal Muscle Leg	muscle
47	chr3:17330200-17331600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:17330200-17333200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:17330200-17333400	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr3:17330200-17333400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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