Variant report

Variant	rs9442946
Chromosome Location	chr6:74406852-74406853
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	SMARCC1	chr6:74404409-74407235	Hela-S3	cervix:	n/a	chr6:74404981-74404990
2	POLR2A	chr6:74405065-74407421	PBDE	blood:	n/a	n/a
3	POLR2A	chr6:74406749-74407122	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr6:74406772-74407262	MCF10A-Er-Src	breast:	n/a	n/a
5	SIN3AK20	chr6:74406772-74407496	MCF-7	breast:	n/a	n/a
6	POLR2A	chr6:74404505-74407290	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:74404585-74407407	MCF10A-Er-Src	breast:	n/a	n/a
8	GATA2	chr6:74406739-74407260	HUVEC	blood vessel:	n/a	n/a
9	NR2F2	chr6:74406794-74407388	MCF-7	breast:	n/a	n/a
10	POLR2A	chr6:74404553-74407749	HUVEC	blood vessel:	n/a	n/a
11	MYC	chr6:74406801-74407118	MCF10A-Er-Src	breast:	n/a	n/a
12	GATA3	chr6:74406827-74407282	MCF-7	breast:	n/a	n/a
13	GATA3	chr6:74406655-74407351	MCF-7	breast:	n/a	n/a
14	GATA3	chr6:74406727-74407405	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:74406472..74407423-chr6:74442579..74443307,2	MCF-7	breast:
2	chr6:74405547..74407236-chr6:76311267..76312799,2	MCF-7	breast:
3	chr6:74405938..74408265-chr6:74438560..74441116,2	MCF-7	breast:
4	chr6:74365580..74367470-chr6:74406292..74408552,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231652	TF binding region
ENSG00000112701	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs55982851	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56171536	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56311419	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72953369	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72953372	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72953375	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9442947	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9442948	0.82[AFR][1000 genomes]
rs9446984	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9446986	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9446988	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
6	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv1029927	chr6:74300496-74424355	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv1027691	chr6:74302980-74417450	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9442946	CD109	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74404600-74407800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:74405000-74407000	Active TSS	A549	lung
3	chr6:74405000-74407200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr6:74405000-74407600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:74405000-74408000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr6:74405200-74407000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:74405200-74407000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:74405200-74407000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:74405200-74407000	Active TSS	Fetal Muscle Trunk	muscle
10	chr6:74405200-74407200	Active TSS	NHDF-Ad	bronchial
11	chr6:74405200-74407400	Active TSS	Right Atrium	heart
12	chr6:74405200-74407600	Active TSS	NHLF	lung
13	chr6:74405400-74407000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr6:74405400-74407000	Active TSS	Right Ventricle	heart
15	chr6:74405400-74407000	Active TSS	GM12878-XiMat	blood
16	chr6:74405400-74407200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
17	chr6:74405600-74407200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:74405800-74407400	Active TSS	Lung	lung
19	chr6:74406000-74407000	Active TSS	Brain Hippocampus Middle	brain
20	chr6:74406000-74407400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr6:74406000-74407400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr6:74406200-74407000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr6:74406200-74407000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr6:74406200-74407000	Flanking Active TSS	Fetal Heart	heart
25	chr6:74406200-74407000	Flanking Active TSS	Fetal Thymus	thymus
26	chr6:74406200-74407000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
27	chr6:74406200-74407400	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr6:74406200-74407600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:74406400-74407000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr6:74406400-74407000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:74406400-74407000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:74406400-74407000	Weak transcription	Left Ventricle	heart
33	chr6:74406400-74407000	Flanking Active TSS	NH-A	brain
34	chr6:74406400-74407200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
35	chr6:74406400-74407200	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr6:74406400-74407200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:74406400-74407200	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr6:74406400-74407200	Flanking Active TSS	Osteobl	bone
39	chr6:74406400-74407400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:74406400-74407600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr6:74406400-74407600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr6:74406400-74407600	Flanking Active TSS	HUVEC	blood vessel
43	chr6:74406600-74407000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:74406600-74407000	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr6:74406600-74407000	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:74406600-74407000	Active TSS	Adipose Nuclei	Adipose
47	chr6:74406600-74407000	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr6:74406600-74407000	Enhancers	HepG2	liver
49	chr6:74406600-74407200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:74406600-74407200	Enhancers	Fetal Lung	lung

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