Variant report

Variant	rs1996971
Chromosome Location	chr6:25222058-25222059
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25217783..25220608-chr6:25221388..25225373,4	K562	blood:
2	chr6:25216145..25218420-chr6:25221724..25223858,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000219681	Chromatin interaction

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]
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]
rs6939764	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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25218200-25223600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr6:25218200-25223800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:25218200-25224000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:25218800-25224000	Weak transcription	Fetal Thymus	thymus
5	chr6:25219000-25223600	Weak transcription	Fetal Brain Female	brain
6	chr6:25219600-25224000	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:25219600-25224200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:25219800-25223400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:25219800-25223400	Weak transcription	Adipose Nuclei	Adipose
10	chr6:25219800-25223800	Weak transcription	HUVEC	blood vessel
11	chr6:25220200-25223800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:25220400-25224000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr6:25220600-25222200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:25220600-25222800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr6:25220800-25223600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr6:25221000-25223600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:25221000-25223800	Weak transcription	NHDF-Ad	bronchial
18	chr6:25221200-25222200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:25221200-25222400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:25221200-25222600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:25221200-25222600	Weak transcription	HMEC	breast
22	chr6:25221400-25222800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:25221400-25223400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:25221400-25223600	Weak transcription	NHEK	skin
25	chr6:25221400-25224000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:25221400-25229200	Weak transcription	Placenta	Placenta
27	chr6:25221400-25229400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:25221600-25223800	Weak transcription	Liver	Liver
29	chr6:25222000-25222800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:25222000-25224400	Enhancers	Hela-S3	cervix

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