Variant report

Variant	rs12204538
Chromosome Location	chr6:16841508-16841509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:16834851..16837013-chr6:16841039..16842548,2	K562	blood:
2	chr6:16762573..16764583-chr6:16841307..16844276,2	MCF-7	breast:
3	chr6:16831439..16834686-chr6:16840301..16843273,3	K562	blood:

Variant related genes	Relation type
ENSG00000272341	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10949386	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961262	0.88[ASN][1000 genomes]
rs1240835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1240839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529203	0.86[ASN][1000 genomes]
rs2797805	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57489962	0.88[ASN][1000 genomes]
rs6459487	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73725256	0.88[ASN][1000 genomes]
rs770931	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs770935	0.83[ASN][1000 genomes]
rs770937	0.83[ASN][1000 genomes]
rs770938	0.81[ASN][1000 genomes]
rs9464950	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464951	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9464952	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9477235	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv1015992	chr6:16469059-16846847	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv538148	chr6:16469059-16846847	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:16837400-16849000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:16837800-16849600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:16838600-16843400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:16838600-16849600	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:16838800-16849600	Weak transcription	Brain Germinal Matrix	brain
6	chr6:16839600-16841800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:16839800-16842000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:16840000-16841800	Enhancers	Fetal Brain Male	brain
9	chr6:16840000-16843600	Enhancers	Placenta Amnion	Placenta Amnion
10	chr6:16840200-16841600	Enhancers	Primary hematopoietic stem cells	blood
11	chr6:16840200-16842200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:16840200-16842400	Enhancers	NHEK	skin
13	chr6:16840400-16841600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr6:16840400-16841600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr6:16840400-16842000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr6:16840400-16842600	Enhancers	Fetal Lung	lung
17	chr6:16840600-16841800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr6:16840600-16842600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:16840800-16841600	Enhancers	NH-A	brain
20	chr6:16840800-16842400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:16841000-16841800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:16841000-16841800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:16841200-16841600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:16841200-16841800	Enhancers	Fetal Brain Female	brain
25	chr6:16841200-16841800	Enhancers	GM12878-XiMat	blood
26	chr6:16841200-16842600	Enhancers	Placenta	Placenta
27	chr6:16841400-16841600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:16841400-16842000	Enhancers	HMEC	breast

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