Variant report

Variant	rs1998885
Chromosome Location	chr14:39898946-39898947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39649512..39652193-chr14:39897469..39900946,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10047876	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10130181	0.85[CHB][hapmap]
rs10133746	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10136490	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10140997	0.85[CHB][hapmap]
rs10142029	0.86[CHB][hapmap]
rs10146106	0.86[CHB][hapmap]
rs10146622	0.85[CHB][hapmap]
rs10220689	0.86[CHB][hapmap]
rs12433987	0.86[CHB][hapmap]
rs12437261	0.86[CHB][hapmap]
rs12883658	0.80[AMR][1000 genomes]
rs12886099	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17109168	0.85[CHB][hapmap]
rs1955716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899887	0.85[CHB][hapmap]
rs4902458	0.86[CHB][hapmap]
rs4902559	0.85[CHB][hapmap]
rs7156962	0.85[CHB][hapmap]
rs7158282	0.86[CHB][hapmap]
rs8006076	0.85[CHB][hapmap]
rs8011412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322999	0.85[CHB][hapmap]
rs9805937	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3523177	chr14:39875036-40128325	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3523178	chr14:39875036-40128325	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv832774	chr14:39897746-40060823	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39886600-39900000	Weak transcription	Esophagus	oesophagus
2	chr14:39886600-39900000	Weak transcription	Pancreas	Pancrea
3	chr14:39886800-39899200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr14:39886800-39899600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr14:39887000-39899200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:39891800-39899000	Weak transcription	Fetal Intestine Small	intestine
7	chr14:39891800-39899000	Weak transcription	Small Intestine	intestine
8	chr14:39893000-39899400	Weak transcription	Fetal Intestine Large	intestine
9	chr14:39895800-39899000	Weak transcription	Spleen	Spleen
10	chr14:39896000-39899000	Weak transcription	Placenta	Placenta
11	chr14:39896000-39899800	Weak transcription	HSMM	muscle
12	chr14:39896000-39900000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:39896000-39900200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr14:39896200-39899000	Weak transcription	Right Atrium	heart
15	chr14:39896200-39899200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr14:39896200-39899200	Weak transcription	Fetal Muscle Leg	muscle
17	chr14:39896400-39899600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr14:39896400-39899600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr14:39896400-39899600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr14:39896400-39899600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr14:39896400-39899800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr14:39896400-39900000	Weak transcription	A549	lung
23	chr14:39897200-39899200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr14:39897200-39900000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr14:39897400-39900000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr14:39897600-39899400	Weak transcription	Left Ventricle	heart
27	chr14:39897600-39899600	Enhancers	Primary B cells from peripheral blood	blood
28	chr14:39897600-39899800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr14:39897600-39900000	Weak transcription	Lung	lung
30	chr14:39897800-39899000	Enhancers	Fetal Brain Female	brain
31	chr14:39897800-39903000	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr14:39898000-39899000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr14:39898000-39899000	Enhancers	Primary hematopoietic stem cells	blood
34	chr14:39898000-39899000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr14:39898000-39899000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr14:39898000-39899000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr14:39898000-39899000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr14:39898000-39899200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr14:39898000-39899400	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr14:39898000-39899600	Enhancers	Fetal Stomach	stomach
41	chr14:39898000-39899800	Enhancers	Liver	Liver
42	chr14:39898000-39900400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr14:39898200-39899400	Flanking Active TSS	GM12878-XiMat	blood
44	chr14:39898200-39899800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr14:39898200-39900000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr14:39898200-39900600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr14:39898400-39899200	Enhancers	HMEC	breast
48	chr14:39898400-39899400	Enhancers	Fetal Kidney	kidney
49	chr14:39898400-39899600	Enhancers	NHEK	skin
50	chr14:39898400-39899800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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