Variant report

Variant	rs2637088
Chromosome Location	chr19:56647406-56647407
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56637204..56640116-chr19:56644041..56647745,4	K562	blood:
2	chr19:56632432..56634662-chr19:56644261..56647544,4	MCF-7	breast:
3	chr19:56645494..56648781-chr19:56650139..56653742,5	K562	blood:
4	chr19:56635952..56638231-chr19:56646331..56649019,3	MCF-7	breast:
5	chr19:56631213..56633451-chr19:56646728..56649320,2	K562	blood:

Variant related genes	Relation type
ENSG00000142409	Chromatin interaction
ENSG00000167685	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs2450439	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2631625	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2631627	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2631628	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2631631	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2631637	0.85[ASN][1000 genomes]
rs2631640	0.81[ASN][1000 genomes]
rs2637092	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2637094	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2637097	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2637114	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2932757	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs473953	0.87[ASN][1000 genomes]
rs478402	0.85[ASN][1000 genomes]
rs490345	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs497453	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs506547	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs517021	0.84[ASN][1000 genomes]
rs522980	0.82[AMR][1000 genomes]
rs524778	0.84[ASN][1000 genomes]
rs524829	0.84[ASN][1000 genomes]
rs524988	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs525827	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs527715	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs544365	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs545570	0.80[AMR][1000 genomes]
rs547002	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs547945	0.83[AMR][1000 genomes]
rs565879	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs569310	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs572851	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs578990	0.84[ASN][1000 genomes]
rs578991	0.87[ASN][1000 genomes]
rs583330	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs587702	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs592827	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs599405	0.87[AMR][1000 genomes]
rs626821	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs628090	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs629544	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs640654	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs643133	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs643174	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs659424	0.86[ASN][1000 genomes]
rs662308	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs662763	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs665082	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs665857	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs667438	0.84[ASN][1000 genomes]
rs667523	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs667974	0.84[ASN][1000 genomes]
rs669866	0.81[ASN][1000 genomes]
rs677127	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs678540	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs684653	0.84[ASN][1000 genomes]
rs8108818	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
11	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers 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	93 gene(s)	inside rSNPs	diseases
12	nsv528361	chr19:56638845-56688570	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 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	chr19:56637800-56647600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:56638600-56651200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr19:56638800-56651800	Weak transcription	Spleen	Spleen
4	chr19:56639000-56647600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:56640800-56649000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr19:56642600-56647800	Enhancers	Placenta	Placenta
7	chr19:56644000-56651200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:56644000-56651200	Weak transcription	Lung	lung
9	chr19:56644000-56651200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:56644200-56647600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:56644200-56647600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:56644200-56647600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:56644200-56647600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr19:56644200-56647600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:56644200-56649400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr19:56644200-56651200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:56644200-56651200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr19:56644200-56651200	Weak transcription	Brain Anterior Caudate	brain
19	chr19:56644200-56651200	Weak transcription	Fetal Kidney	kidney
20	chr19:56644200-56651400	Weak transcription	Right Atrium	heart
21	chr19:56644400-56651200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:56644800-56649000	Weak transcription	Adipose Nuclei	Adipose
23	chr19:56645000-56647600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr19:56645000-56651200	Weak transcription	Aorta	Aorta
25	chr19:56645200-56647600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr19:56645400-56651200	Weak transcription	NH-A	brain
27	chr19:56645400-56651800	Enhancers	Pancreas	Pancrea
28	chr19:56645600-56647600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:56645800-56647600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr19:56645800-56647800	Weak transcription	Colonic Mucosa	Colon
31	chr19:56645800-56648800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr19:56645800-56648800	Weak transcription	A549	lung
33	chr19:56645800-56649000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:56645800-56651200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:56645800-56651200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr19:56645800-56651200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:56645800-56651200	Weak transcription	HSMM	muscle
38	chr19:56645800-56651400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:56645800-56651600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr19:56646000-56647600	Weak transcription	K562	blood
41	chr19:56646000-56648800	Weak transcription	Fetal Lung	lung
42	chr19:56646000-56651200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:56646000-56651200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:56646000-56651200	Weak transcription	Fetal Brain Female	brain
45	chr19:56646000-56651200	Weak transcription	Fetal Muscle Leg	muscle
46	chr19:56646000-56651200	Weak transcription	HSMMtube	muscle
47	chr19:56646000-56651200	Weak transcription	NHDF-Ad	bronchial
48	chr19:56646000-56651200	Weak transcription	Osteobl	bone
49	chr19:56646000-56651400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:56646000-56651600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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