Variant report

Variant	rs12200354
Chromosome Location	chr6:24673803-24673804
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24673294..24675944-chr6:24718110..24721805,3	K562	blood:
2	chr6:24667206..24668825-chr6:24671438..24674549,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112308	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000111802	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10946716	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12194181	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205123	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12214093	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212231	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6915781	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6916159	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6916165	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6916608	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6928074	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6936786	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6937517	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9358788	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9358789	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358790	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393577	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9393578	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393579	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][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	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24668000-24676000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:24668200-24674400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:24668200-24699800	Weak transcription	Brain Substantia Nigra	brain
4	chr6:24668800-24691800	Weak transcription	Psoas Muscle	Psoas
5	chr6:24669000-24675800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:24669000-24681800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:24669000-24686400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:24669000-24690400	Weak transcription	Gastric	stomach
9	chr6:24669000-24693000	Weak transcription	Primary T cells from cord blood	blood
10	chr6:24669000-24701200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:24669200-24675800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr6:24669200-24686200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:24669200-24690800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:24669400-24687600	Weak transcription	Left Ventricle	heart
15	chr6:24669400-24701600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr6:24671400-24687200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:24671800-24675600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
18	chr6:24672000-24674800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
19	chr6:24672600-24674800	ZNF genes & repeats	Fetal Intestine Small	intestine
20	chr6:24673000-24674800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:24673000-24675400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
22	chr6:24673200-24674400	Enhancers	Liver	Liver
23	chr6:24673600-24674800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:24673800-24674800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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