Variant report

Variant	rs6699507
Chromosome Location	chr1:209952346-209952347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:209940700-209952492	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209950429..209953463-chr1:209956092..209959569,7	K562	blood:
2	chr1:209947985..209951764-chr1:209952095..209954768,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSD11B1-3	chr1:209951712-209953951	NONHSAT009244

Variant related genes	Relation type
TRAF3IP3	TF binding region
ENSG00000162757	Chromatin interaction
ENSG00000009790	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10127937	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10218448	0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10489344	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11119344	0.84[CEU][hapmap]
rs11119354	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11582607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11584081	0.88[JPT][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11590807	1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810091	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12403006	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12404886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17317580	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17389541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2013196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28601717	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34743335	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3753510	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3753513	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3766615	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs41274838	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4240837	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56071308	0.84[ASN][1000 genomes]
rs56268268	0.85[ASN][1000 genomes]
rs72741048	0.82[EUR][1000 genomes]
rs7526313	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544804	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs932334	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6699507	IRF6	cis	Whole Blood	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209942800-209956800	Weak transcription	Small Intestine	intestine
2	chr1:209942800-209957200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:209943400-209952600	Weak transcription	Fetal Intestine Small	intestine
4	chr1:209943600-209956600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:209943800-209954600	Weak transcription	NHEK	skin
6	chr1:209943800-209956600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:209943800-209956600	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:209943800-209957000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:209943800-209957200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:209944000-209952800	Weak transcription	HMEC	breast
11	chr1:209944000-209956000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:209944000-209956600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:209944600-209954400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:209944800-209955200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:209944800-209956600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:209944800-209956600	Weak transcription	Right Ventricle	heart
17	chr1:209945000-209953400	Weak transcription	Liver	Liver
18	chr1:209945000-209953600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:209945000-209953800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:209945000-209956000	Weak transcription	Brain Anterior Caudate	brain
21	chr1:209945000-209956400	Weak transcription	Left Ventricle	heart
22	chr1:209945000-209956600	Weak transcription	Adipose Nuclei	Adipose
23	chr1:209945000-209956600	Weak transcription	Brain Angular Gyrus	brain
24	chr1:209945000-209956600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:209945000-209956600	Weak transcription	Esophagus	oesophagus
26	chr1:209945000-209956600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:209945000-209956800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:209945000-209956800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:209945200-209954600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:209945200-209956600	Weak transcription	Colonic Mucosa	Colon
31	chr1:209945200-209956600	Weak transcription	Pancreas	Pancrea
32	chr1:209945200-209957200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:209945400-209954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:209945400-209956400	Weak transcription	Lung	lung
35	chr1:209945600-209955800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:209945600-209956400	Weak transcription	Gastric	stomach
37	chr1:209945600-209956600	Weak transcription	Fetal Lung	lung
38	chr1:209945800-209956600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:209946000-209955800	Weak transcription	K562	blood
40	chr1:209946000-209956000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:209946000-209956600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:209946000-209956600	Strong transcription	Fetal Thymus	thymus
43	chr1:209946200-209954600	Weak transcription	Fetal Stomach	stomach
44	chr1:209946200-209956600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:209946400-209956000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:209946400-209956800	Strong transcription	Primary hematopoietic stem cells	blood
47	chr1:209946600-209956400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:209947200-209956400	Strong transcription	Dnd41	blood
49	chr1:209947600-209956600	Strong transcription	Thymus	Thymus
50	chr1:209948800-209956200	Strong transcription	Primary monocytes fromperipheralblood	blood

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