Variant report

Variant	rs3909109
Chromosome Location	chr6:31096367-31096368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31081982..31084650-chr6:31092935..31096389,3	MCF-7	breast:
2	chr6:31090987..31092952-chr6:31095057..31097204,2	K562	blood:
3	chr6:31096272..31098669-chr6:31109725..31111701,2	MCF-7	breast:
4	chr6:31095559..31096550-chr6:31334364..31334869,2	K562	blood:
5	chr6:30884097..30886583-chr6:31095164..31097227,2	K562	blood:
6	chr6:31093740..31096659-chr6:31097265..31098967,2	K562	blood:
7	chr6:31095053..31098000-chr6:31105579..31108492,2	K562	blood:
8	chr6:31086431..31090113-chr6:31095332..31098474,3	K562	blood:
9	chr6:31093836..31097468-chr6:31099358..31102420,4	K562	blood:
10	chr6:31075272..31076774-chr6:31094558..31097353,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137411	Chromatin interaction
ENSG00000204539	Chromatin interaction
ENSG00000204538	Chromatin interaction
ENSG00000204540	Chromatin interaction
ENSG00000228432	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs3815087	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3909110	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6911408	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6931464	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6931633	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6932435	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9263699	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9263701	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9263703	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9263715	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9263716	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9263717	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv1033227	chr6:31071547-31101674	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv884137	chr6:31082361-31129310	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
14	esv1820685	chr6:31083813-31097453	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	esv1799829	chr6:31087133-31097183	Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	esv33699	chr6:31094845-31110011	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3909109	PSORS1C1	cis	Thyroid	GTEx
rs3909109	PSORS1C1	cis	Skin Sun Exposed Lower leg	GTEx
rs3909109	PSORS1C1	cis	Artery Tibial	GTEx
rs3909109	PSORS1C2	cis	Artery Tibial	GTEx
rs3909109	PSORS1C2	cis	lung	GTEx
rs3909109	PSORS1C1	cis	Adipose Subcutaneous	GTEx
rs3909109	PSORS1C2	cis	Thyroid	GTEx
rs3909109	PSORS1C1	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31083200-31105400	Weak transcription	Spleen	Spleen
2	chr6:31093200-31096600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:31093400-31105400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:31093400-31107000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:31093800-31097800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr6:31094000-31097000	Weak transcription	Pancreas	Pancrea
7	chr6:31094600-31099400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:31094800-31097000	Weak transcription	Esophagus	oesophagus
9	chr6:31095000-31096400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:31095000-31097200	Weak transcription	Left Ventricle	heart
11	chr6:31095000-31105400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:31095000-31105400	Weak transcription	HMEC	breast
13	chr6:31095600-31097400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr6:31095800-31096400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr6:31095800-31096400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr6:31095800-31096400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:31095800-31096400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr6:31095800-31096400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:31095800-31097000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr6:31096000-31096400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr6:31096000-31096400	Weak transcription	NHEK	skin
22	chr6:31096000-31097000	Weak transcription	GM12878-XiMat	blood
23	chr6:31096000-31101000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:31096000-31105400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr6:31096000-31107000	Weak transcription	Right Atrium	heart
26	chr6:31096200-31096400	Bivalent Enhancer	Primary B cells from peripheral blood	blood

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