Variant report

Variant	rs12616940
Chromosome Location	chr2:172252217-172252218
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	chr2:172251047..172252605-chr2:172289597..172292049,2	K562	blood:

Variant related genes	Relation type
ENSG00000115827	Chromatin interaction
ENSG00000123600	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10460358	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10930473	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11677562	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11679641	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12052810	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12465868	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12469151	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12471094	0.83[AMR][1000 genomes]
rs1558963	0.86[ASN][1000 genomes]
rs17285260	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1921776	0.83[AMR][1000 genomes]
rs2356709	0.80[ASN][1000 genomes]
rs4667685	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55862836	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62181358	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62183460	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66893860	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6747400	0.86[ASN][1000 genomes]
rs7590275	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs997666	0.84[AMR][1000 genomes];0.80[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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172222200-172289600	Weak transcription	Gastric	stomach
2	chr2:172232000-172253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:172237800-172254400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr2:172238000-172272400	Weak transcription	Fetal Intestine Large	intestine
5	chr2:172238800-172272400	Weak transcription	Primary T cells from cord blood	blood
6	chr2:172239200-172257400	Weak transcription	K562	blood
7	chr2:172243600-172253400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:172243800-172257800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:172244000-172257800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:172246800-172255400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr2:172247200-172254200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:172248000-172266000	Weak transcription	Left Ventricle	heart
13	chr2:172248200-172257600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:172248200-172258000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:172248400-172257000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:172248400-172258000	Weak transcription	NHEK	skin
17	chr2:172248400-172258400	Weak transcription	HSMM	muscle
18	chr2:172248400-172259600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:172248400-172259600	Weak transcription	Hela-S3	cervix
20	chr2:172248600-172265400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:172248800-172258000	Weak transcription	A549	lung
22	chr2:172249000-172258400	Weak transcription	HepG2	liver
23	chr2:172249000-172259200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:172250000-172252600	Enhancers	GM12878-XiMat	blood
25	chr2:172250000-172253800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:172250200-172252400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr2:172250800-172255800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:172251600-172256800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr2:172251600-172256800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr2:172251800-172253800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:172251800-172256000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:172252000-172256600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:172252000-172256800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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