Variant report

Variant	rs16846397
Chromosome Location	chr1:173725356-173725357
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	chr1:173718954..173722251-chr1:173724534..173727033,3	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1322769	1.00[AMR][1000 genomes]
rs16846483	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2227620	1.00[AMR][1000 genomes]
rs57006357	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57343517	1.00[AMR][1000 genomes]
rs57832781	1.00[AMR][1000 genomes]
rs58425101	1.00[AMR][1000 genomes]
rs58576036	1.00[AMR][1000 genomes]
rs58930477	1.00[AMR][1000 genomes]
rs59355797	1.00[AMR][1000 genomes]
rs61075186	1.00[AMR][1000 genomes]
rs6667627	1.00[AMR][1000 genomes]
rs6691086	1.00[AMR][1000 genomes]
rs6704413	1.00[AMR][1000 genomes]
rs73025495	1.00[AMR][1000 genomes]
rs73025612	1.00[AMR][1000 genomes]
rs73025620	1.00[AMR][1000 genomes]
rs73027303	1.00[AMR][1000 genomes]
rs73027364	1.00[AMR][1000 genomes]
rs73027398	1.00[AMR][1000 genomes]
rs73029321	1.00[AMR][1000 genomes]
rs73035116	1.00[AMR][1000 genomes]
rs73035134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73035139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73037076	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73037083	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73037097	1.00[AMR][1000 genomes]
rs73041050	1.00[AMR][1000 genomes]
rs73041059	1.00[AMR][1000 genomes]
rs7519571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7531236	1.00[AMR][1000 genomes]
rs7539992	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9726181	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv3598	chr1:173693027-173738687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173686800-173725400	Weak transcription	Right Ventricle	heart
2	chr1:173695400-173726000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:173695800-173726000	Weak transcription	Esophagus	oesophagus
4	chr1:173695800-173729800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:173696200-173726000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:173699600-173725800	Weak transcription	Fetal Kidney	kidney
7	chr1:173703400-173726000	Weak transcription	Aorta	Aorta
8	chr1:173703400-173726000	Weak transcription	Spleen	Spleen
9	chr1:173703400-173726000	Weak transcription	NHEK	skin
10	chr1:173703800-173728200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:173705800-173725400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:173710200-173726000	Weak transcription	Brain Germinal Matrix	brain
13	chr1:173713400-173731600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:173718800-173725800	Weak transcription	A549	lung
15	chr1:173720000-173730000	Strong transcription	Primary B cells from cord blood	blood
16	chr1:173720000-173730600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:173720200-173727400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:173720200-173728000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:173720200-173729000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:173720200-173729000	Strong transcription	Dnd41	blood
21	chr1:173720200-173729600	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:173720200-173729800	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:173720200-173730000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:173720200-173730200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr1:173720400-173726000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:173720400-173727000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:173720400-173729800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:173720600-173728000	Weak transcription	Stomach Mucosa	stomach
29	chr1:173720600-173728600	Strong transcription	Hela-S3	cervix
30	chr1:173720600-173729000	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:173720800-173727200	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:173720800-173728800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:173720800-173728800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:173720800-173728800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:173720800-173729000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:173720800-173729000	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr1:173720800-173729200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:173720800-173729400	Strong transcription	Primary T cells from cord blood	blood
39	chr1:173720800-173729600	Strong transcription	Adipose Nuclei	Adipose
40	chr1:173720800-173729800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:173720800-173729800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:173720800-173729800	Strong transcription	Fetal Thymus	thymus
43	chr1:173720800-173730000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr1:173720800-173730000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:173721000-173727400	Strong transcription	Fetal Intestine Small	intestine
46	chr1:173721000-173728200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:173721000-173729000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:173721000-173729600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:173721000-173730400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:173721200-173728200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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