Variant report

Variant	rs2420371
Chromosome Location	chr1:169491555-169491556
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169454600..169456893-chr1:169491518..169494069,2	MCF-7	breast:
2	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
3	chr1:169481912..169483495-chr1:169489878..169491578,2	MCF-7	breast:
4	chr1:169485665..169489624-chr1:169491207..169493940,4	K562	blood:
5	chr1:169490192..169493609-chr1:169495804..169500257,7	MCF-7	breast:
6	chr1:169486047..169488375-chr1:169489755..169492077,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117479	Chromatin interaction
ENSG00000213062	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1018827	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap]
rs10737547	0.85[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2213868	0.88[AMR][1000 genomes]
rs2420370	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2420372	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4264045	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6009	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs6025	1.00[CHD][hapmap]
rs6427194	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6427195	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6427196	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6427197	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6670848	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6682179	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6687813	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9332666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs970740	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv872533	chr1:169490401-169508576	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Hemostatic factors and hematological phenotypes	22443383	GWAS catalog

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169481800-169493000	Strong transcription	Liver	Liver
2	chr1:169483200-169495400	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:169483200-169496800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr1:169483800-169496800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr1:169484200-169494400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:169484800-169501000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:169485400-169510600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:169486600-169494400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:169487400-169501000	Weak transcription	Right Ventricle	heart
10	chr1:169488000-169492800	Weak transcription	Hela-S3	cervix
11	chr1:169488000-169493000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:169489800-169492000	Strong transcription	Placenta	Placenta
13	chr1:169489800-169494600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:169490600-169496200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:169490800-169491600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:169490800-169492400	Weak transcription	Stomach Mucosa	stomach
17	chr1:169490800-169492600	Weak transcription	HepG2	liver
18	chr1:169490800-169494600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:169490800-169496200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:169490800-169496800	Weak transcription	Pancreas	Pancrea
21	chr1:169490800-169496800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:169491200-169491800	Weak transcription	Fetal Intestine Large	intestine
23	chr1:169491200-169497000	Weak transcription	Small Intestine	intestine

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