Variant report

Variant	rs2209993
Chromosome Location	chr20:13758061-13758062
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:13757853..13760208-chr20:13761731..13763400,2	MCF-7	breast:
2	chr20:13756538..13758673-chr20:13764158..13765798,2	MCF-7	breast:
3	chr20:13754204..13756033-chr20:13757365..13759391,2	K562	blood:
4	chr20:13754533..13756857-chr20:13757321..13759391,2	K562	blood:

Variant related genes	Relation type
ENSG00000089048	Chromatin interaction
ENSG00000101247	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs13039364	0.88[CHB][hapmap]
rs13042637	0.84[ASN][1000 genomes]
rs1547920	0.91[ASN][1000 genomes]
rs1999112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2031933	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2094651	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2209994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327797	0.88[CHB][hapmap]
rs2423745	0.97[ASN][1000 genomes]
rs2423749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2423750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2423753	0.86[ASN][1000 genomes]
rs3180370	0.91[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34449907	0.90[ASN][1000 genomes]
rs34806363	0.90[ASN][1000 genomes]
rs35361761	0.81[ASN][1000 genomes]
rs35632254	0.81[ASN][1000 genomes]
rs3789339	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4813139	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs4813141	0.83[EUR][1000 genomes]
rs4813142	0.93[ASN][1000 genomes]
rs4814256	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4814258	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6033809	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6033816	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6033819	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033820	0.86[AFR][1000 genomes]
rs6033821	0.91[CEU][hapmap];0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6042324	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6042336	0.95[CEU][hapmap];0.88[CHB][hapmap]
rs6042347	0.89[EUR][1000 genomes]
rs6042351	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6042352	0.87[AFR][1000 genomes]
rs6042357	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6042362	0.97[ASN][1000 genomes]
rs6074637	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs6074643	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs6074644	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs6079154	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs6079156	0.86[CHB][hapmap]
rs6079158	0.88[CHB][hapmap]
rs6079162	0.91[CEU][hapmap];0.88[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6079165	0.84[ASN][1000 genomes]
rs6079166	0.88[CHB][hapmap];0.91[ASN][1000 genomes]
rs6079176	0.90[ASN][1000 genomes]
rs6079178	0.90[ASN][1000 genomes]
rs6079181	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs6079182	0.86[ASN][1000 genomes]
rs6105162	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6110026	0.92[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6110035	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6134968	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62209178	0.84[ASN][1000 genomes]
rs62209207	0.90[ASN][1000 genomes]
rs68012295	0.91[ASN][1000 genomes]
rs7265467	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs754796	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' 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
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13694600-13764400	Weak transcription	Stomach Mucosa	stomach
2	chr20:13734000-13763200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr20:13736800-13763800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr20:13741800-13763200	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr20:13741800-13763800	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr20:13742000-13759000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr20:13742000-13762600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr20:13742200-13763600	Strong transcription	Liver	Liver
9	chr20:13742400-13763800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr20:13743800-13758200	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr20:13743800-13763600	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr20:13744000-13758200	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr20:13744400-13758600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr20:13744400-13763200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr20:13747200-13758200	Strong transcription	A549	lung
16	chr20:13747200-13759400	Strong transcription	HepG2	liver
17	chr20:13747200-13764000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr20:13747600-13758600	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr20:13747600-13759000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr20:13747600-13759200	Strong transcription	Fetal Intestine Large	intestine
21	chr20:13747600-13764400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr20:13747800-13759000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr20:13747800-13763800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr20:13748000-13759000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr20:13748000-13763200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr20:13748000-13763800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr20:13748400-13764000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr20:13748600-13763400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr20:13748800-13763800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr20:13748800-13764200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr20:13749000-13760600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr20:13749000-13764000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr20:13749000-13764200	Weak transcription	Aorta	Aorta
34	chr20:13749000-13764200	Weak transcription	Colonic Mucosa	Colon
35	chr20:13749000-13765200	Weak transcription	Small Intestine	intestine
36	chr20:13749200-13764200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr20:13749200-13764200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr20:13749800-13764000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr20:13750200-13760400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr20:13750400-13760600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr20:13750400-13764200	Weak transcription	Pancreas	Pancrea
42	chr20:13750400-13764200	Weak transcription	Spleen	Spleen
43	chr20:13750600-13764200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr20:13750600-13764200	Weak transcription	Thymus	Thymus
45	chr20:13750600-13765000	Weak transcription	Gastric	stomach
46	chr20:13751200-13760200	Weak transcription	Lung	lung
47	chr20:13751200-13765000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr20:13751400-13759400	Weak transcription	Fetal Intestine Small	intestine
49	chr20:13751400-13760600	Weak transcription	Left Ventricle	heart
50	chr20:13751400-13761800	Weak transcription	Fetal Stomach	stomach

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