Variant report

Variant	rs2187939
Chromosome Location	chr1:174977407-174977408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174973381..174976191-chr1:174977396..174979705,2	MCF-7	breast:
2	chr1:174976375..174978971-chr1:174983960..174985609,2	MCF-7	breast:
3	chr1:174973206..174975199-chr1:174975855..174978492,3	MCF-7	breast:
4	chr1:174966455..174979047-chr1:174985921..174994239,29	MCF-7	breast:
5	chr1:174975701..174977916-chr1:174990172..174992601,2	MCF-7	breast:
6	chr1:174966903..174971287-chr1:174971534..174977740,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120333	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000206659	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1046439	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801791	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978053	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1984418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105949	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2285208	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285210	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2301507	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3753563	0.84[AFR][1000 genomes]
rs4651238	0.82[ASN][1000 genomes]
rs6425309	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425310	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6669560	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66700013	0.82[ASN][1000 genomes]
rs7514888	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001000	chr1:174944208-174978853	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174969800-174981600	Weak transcription	Gastric	stomach
2	chr1:174970000-174982400	Weak transcription	Esophagus	oesophagus
3	chr1:174970000-174991800	Weak transcription	Stomach Mucosa	stomach
4	chr1:174970200-174981200	Weak transcription	Right Ventricle	heart
5	chr1:174970600-174981800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:174970800-174980800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:174970800-174986000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:174971000-174991600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:174971800-174977800	Weak transcription	Fetal Heart	heart
10	chr1:174972000-174981000	Weak transcription	Fetal Intestine Small	intestine
11	chr1:174972600-174981800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:174973000-174982200	Weak transcription	Fetal Brain Male	brain
13	chr1:174973000-174990600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:174973200-174978600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:174973200-174982000	Weak transcription	Small Intestine	intestine
16	chr1:174973200-174983600	Strong transcription	K562	blood
17	chr1:174973200-174987800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:174973200-174987800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:174973200-174988200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:174973600-174987800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:174973600-174988200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:174973600-174990400	Strong transcription	Primary T cells from cord blood	blood
23	chr1:174973800-174980600	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr1:174973800-174983800	Strong transcription	NH-A	brain
25	chr1:174973800-174984000	Strong transcription	Hela-S3	cervix
26	chr1:174973800-174984600	Strong transcription	NHDF-Ad	bronchial
27	chr1:174973800-174987600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:174973800-174987800	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr1:174973800-174987800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:174973800-174987800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:174973800-174987800	Strong transcription	Fetal Intestine Large	intestine
32	chr1:174973800-174987800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:174973800-174988200	Strong transcription	Primary hematopoietic stem cells	blood
34	chr1:174973800-174988400	Strong transcription	Fetal Thymus	thymus
35	chr1:174973800-174988800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr1:174973800-174988800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:174973800-174989800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:174974000-174978000	Strong transcription	Left Ventricle	heart
39	chr1:174974000-174987800	Strong transcription	Liver	Liver
40	chr1:174974000-174988200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:174974000-174988400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:174974200-174978000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:174974200-174979800	Strong transcription	Fetal Brain Female	brain
44	chr1:174974200-174980000	Strong transcription	Primary B cells from cord blood	blood
45	chr1:174974200-174980000	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr1:174974200-174984000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:174974200-174984400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:174974200-174985200	Strong transcription	Fetal Muscle Leg	muscle
49	chr1:174974200-174987600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:174974200-174987800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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