Variant report

Variant	rs6698799
Chromosome Location	chr1:224806555-224806556
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	chr1:224805248..224807412-chr1:224827891..224830752,2	K562	blood:
2	chr1:224806254..224809054-chr1:224817462..224819155,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs56039603	0.89[EUR][1000 genomes]
rs56403019	0.95[EUR][1000 genomes]
rs6661853	0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs6664616	0.95[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs6672413	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6672806	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6695959	0.89[ASN][1000 genomes]
rs880496	0.86[CEU][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes]
rs904506	0.97[EUR][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	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6698799	CNIH3	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224803200-224807000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:224803200-224807000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr1:224803200-224807200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:224803200-224807400	Active TSS	NHDF-Ad	bronchial
5	chr1:224803400-224806800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
6	chr1:224803800-224807800	Active TSS	NH-A	brain
7	chr1:224804600-224806600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
8	chr1:224804800-224807000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
9	chr1:224805000-224806600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
10	chr1:224805000-224807000	Bivalent/Poised TSS	Osteobl	bone
11	chr1:224805400-224807400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:224805400-224808000	Flanking Active TSS	Dnd41	blood
13	chr1:224805600-224806800	Bivalent Enhancer	Primary T cells from cord blood	blood
14	chr1:224805600-224807200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:224805800-224806800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr1:224805800-224812200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:224806000-224807000	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:224806000-224808800	Bivalent/Poised TSS	Fetal Brain Female	brain
19	chr1:224806000-224811800	Weak transcription	Spleen	Spleen
20	chr1:224806200-224806600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr1:224806200-224806600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:224806200-224806800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
23	chr1:224806200-224808000	Active TSS	NHLF	lung
24	chr1:224806200-224810400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:224806200-224810400	Weak transcription	Pancreas	Pancrea
26	chr1:224806400-224806600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:224806400-224806600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:224806400-224806600	Active TSS	HMEC	breast
29	chr1:224806400-224806800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:224806400-224807400	Active TSS	Brain Hippocampus Middle	brain

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