Variant report

Variant	rs12199405
Chromosome Location	chr6:106525918-106525919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:106523930..106526144-chr6:106531959..106534268,2	K562	blood:
2	chr6:106524677..106527761-chr6:106528087..106531603,5	K562	blood:
3	chr6:106511817..106514767-chr6:106525243..106527594,2	K562	blood:
4	chr6:106525524..106527475-chr6:106529699..106532511,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRDM1-1	chr6:106525744-106526041	XLOC_005410

Variant related genes	Relation type
ENSG00000057657	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10499050	1.00[YRI][hapmap]
rs11152958	1.00[EUR][1000 genomes]
rs13200402	1.00[YRI][hapmap]
rs6931212	0.96[EUR][1000 genomes]
rs6931248	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1025231	chr6:106451012-106634389	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv830755	chr6:106461705-106624202	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106518000-106530000	Weak transcription	NHEK	skin
2	chr6:106518600-106530400	Strong transcription	Fetal Intestine Small	intestine
3	chr6:106519000-106528000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:106524000-106526600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:106524600-106526400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:106524600-106527200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:106524800-106526000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:106524800-106526400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:106525000-106526000	Enhancers	NHDF-Ad	bronchial
10	chr6:106525000-106526200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:106525000-106526200	Enhancers	NHLF	lung
12	chr6:106525000-106527800	Weak transcription	Brain Germinal Matrix	brain
13	chr6:106525200-106526600	Enhancers	K562	blood
14	chr6:106525400-106526000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:106525400-106530400	Weak transcription	NH-A	brain
16	chr6:106525400-106530600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:106525600-106526000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:106525600-106529200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:106525600-106530600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:106525600-106530800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:106525800-106526000	Enhancers	A549	lung
22	chr6:106525800-106528400	Strong transcription	Fetal Intestine Large	intestine

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