Variant report

Variant	rs6917419
Chromosome Location	chr6:27243480-27243481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27099008..27100568-chr6:27243071..27244881,2	K562	blood:
2	chr6:27218922..27222706-chr6:27243224..27246037,3	K562	blood:
3	chr6:27116703..27118888-chr6:27241856..27243743,2	MCF-7	breast:
4	chr6:27241687..27243656-chr6:27245382..27246993,2	K562	blood:
5	chr6:27216098..27217908-chr6:27241472..27244075,2	K562	blood:

Variant related genes	Relation type
ENSG00000112812	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12153912	0.91[CEU][hapmap]
rs12189835	0.91[CEU][hapmap]
rs12192049	0.91[CEU][hapmap]
rs12193820	0.82[CEU][hapmap]
rs12196084	0.91[CEU][hapmap]
rs12198077	0.91[CEU][hapmap]
rs12201774	0.91[CEU][hapmap]
rs12203728	0.91[CEU][hapmap]
rs12204768	0.81[CEU][hapmap]
rs12205921	0.91[CEU][hapmap]
rs12209393	0.91[CEU][hapmap]
rs12209429	0.91[CEU][hapmap]
rs12209456	0.91[CEU][hapmap]
rs12214930	0.91[CEU][hapmap]
rs16894368	0.80[LWK][hapmap]
rs16894783	0.86[LWK][hapmap]
rs3531	0.91[CEU][hapmap]
rs4636015	0.91[CEU][hapmap]
rs5030955	0.81[CEU][hapmap]
rs67310631	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6902012	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6938397	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7759694	0.82[JPT][hapmap]
rs858984	0.82[CEU][hapmap]
rs858985	0.82[CEU][hapmap]
rs858986	0.91[CEU][hapmap]
rs858989	0.82[CEU][hapmap]
rs858992	0.82[CEU][hapmap]
rs858995	0.91[CEU][hapmap]
rs9295732	1.00[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs9348752	0.80[CEU][hapmap]
rs9348756	1.00[JPT][hapmap]
rs9348759	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs9366690	1.00[JPT][hapmap]
rs9368492	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9368493	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9368494	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9368498	0.82[EUR][1000 genomes]
rs9368499	0.82[EUR][1000 genomes]
rs9368500	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs9379965	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9379967	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9379970	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9379975	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs9393795	0.82[JPT][hapmap]
rs9393796	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9393802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393803	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9468025	0.84[AFR][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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6917419	ZNF323	cis	cerebellum	SCAN
rs6917419	ZNF391	cis	cerebellum	SCAN
rs6917419	ZSCAN23	cis	cerebellum	SCAN
rs6917419	BTN3A3	cis	cerebellum	SCAN
rs6917419	BTN3A2	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27242600-27243800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:27242600-27243800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:27242600-27243800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:27242600-27243800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:27242800-27243800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr6:27242800-27243800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:27242800-27243800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:27243000-27243600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:27243000-27243600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:27243000-27247400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:27243200-27243800	Flanking Active TSS	NHEK	skin
12	chr6:27243400-27243600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:27243400-27243600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:27243400-27243600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:27243400-27243600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
16	chr6:27243400-27243600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:27243400-27243600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:27243400-27243600	Bivalent Enhancer	GM12878-XiMat	blood
19	chr6:27243400-27243600	Bivalent Enhancer	HSMM	muscle
20	chr6:27243400-27243600	Flanking Active TSS	K562	blood
21	chr6:27243400-27243800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr6:27243400-27243800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:27243400-27243800	Flanking Active TSS	A549	lung
24	chr6:27243400-27244200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr6:27243400-27244400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr6:27243400-27244800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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