Variant report

Variant	rs6939764
Chromosome Location	chr6:25219230-25219231
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	chr6:25215050..25216890-chr6:25218996..25221724,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC16A-4	chr6:25218916-25219297	NONHSAT108145

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs188567	1.00[CHB][hapmap]
rs1996971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328866	0.81[AFR][1000 genomes]
rs2328871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328872	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398725	0.83[AFR][1000 genomes]
rs6918771	1.00[CHB][hapmap]
rs6939460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379734	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv462663	chr6:25156197-25234884	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv601167	chr6:25156197-25234884	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv883483	chr6:25200842-25272435	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25215800-25219600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:25216600-25219600	Weak transcription	Hela-S3	cervix
3	chr6:25217600-25219600	Enhancers	Fetal Muscle Leg	muscle
4	chr6:25217800-25220200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr6:25218000-25219400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:25218200-25219800	Weak transcription	NHDF-Ad	bronchial
7	chr6:25218200-25219800	Flanking Active TSS	NHEK	skin
8	chr6:25218200-25220200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:25218200-25223600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:25218200-25223800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:25218200-25224000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:25218400-25219400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:25218400-25219600	Enhancers	Fetal Muscle Trunk	muscle
14	chr6:25218600-25219600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:25218600-25221200	Enhancers	HMEC	breast
16	chr6:25218800-25224000	Weak transcription	Fetal Thymus	thymus
17	chr6:25219000-25220200	Enhancers	Placenta	Placenta
18	chr6:25219000-25221000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr6:25219000-25221400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:25219000-25221400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:25219000-25223600	Weak transcription	Fetal Brain Female	brain
22	chr6:25219200-25219600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:25219200-25221400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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