Variant report

Variant	rs17030909
Chromosome Location	chr4:102140128-102140129
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102134665..102137558-chr4:102138391..102140699,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1472826	1.00[YRI][hapmap]
rs1561720	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030955	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030957	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17031008	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17031015	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs17031073	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17031085	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2659526	1.00[YRI][hapmap]
rs2851007	1.00[YRI][hapmap]
rs58097646	1.00[AMR][1000 genomes]
rs7678617	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 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	chr4:102129000-102140400	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr4:102131800-102146000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:102133000-102143800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:102133000-102143800	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:102133200-102142400	Weak transcription	HSMM	muscle
6	chr4:102133200-102143600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:102135800-102145200	Weak transcription	Small Intestine	intestine
8	chr4:102136000-102141600	Weak transcription	Stomach Mucosa	stomach
9	chr4:102136000-102144400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:102136000-102145800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:102138200-102140400	Enhancers	NHDF-Ad	bronchial
12	chr4:102138400-102140200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr4:102138400-102140600	Enhancers	Osteobl	bone
14	chr4:102138400-102141200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:102138400-102144800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:102138600-102140600	Enhancers	HUVEC	blood vessel
17	chr4:102138800-102140200	Enhancers	Brain Cingulate Gyrus	brain
18	chr4:102138800-102140200	Enhancers	NHLF	lung
19	chr4:102138800-102140400	Enhancers	Brain Substantia Nigra	brain
20	chr4:102138800-102140400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr4:102138800-102140600	Enhancers	Brain Anterior Caudate	brain
22	chr4:102139000-102140400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:102139000-102140400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:102139000-102140400	Enhancers	Brain Hippocampus Middle	brain
25	chr4:102139200-102144000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:102139200-102144000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:102139200-102145600	Weak transcription	Ovary	ovary
28	chr4:102139400-102140200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:102139400-102152000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:102139600-102142000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:102139800-102140200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:102139800-102140400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:102139800-102140400	Flanking Active TSS	A549	lung
34	chr4:102140000-102140200	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr4:102140000-102140200	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr4:102140000-102140400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr4:102140000-102140400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr4:102140000-102140400	Enhancers	Brain Angular Gyrus	brain
39	chr4:102140000-102140600	Enhancers	Fetal Intestine Large	intestine
40	chr4:102140000-102141000	Enhancers	Duodenum Mucosa	Duodenum
41	chr4:102140000-102141800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr4:102140000-102144600	Enhancers	Pancreatic Islets	Pancreatic Islet

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