Variant report

Variant	rs2517425
Chromosome Location	chr6:30949670-30949671
allele	A/C
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	TEAD4	chr6:30949612-30949988	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr6:30949660-30949810	HMEC	breast:	n/a	n/a
3	RAD21	chr6:30949584-30950064	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr6:30949670-30949935	K562	blood:	n/a	chr6:30949880-30949893
5	CTCF	chr6:30949640-30949790	HFF-Myc	foreskin:	n/a	n/a
6	CTCF	chr6:30949645-30949961	MCF-7	breast:	n/a	chr6:30949880-30949893
7	STAT3	chr6:30949638-30950190	MCF10A-Er-Src	breast:	n/a	chr6:30949972-30949981 chr6:30949973-30949982 chr6:30949971-30949982
8	CTCF	chr6:30949639-30950025	H1-hESC	embryonic stem cell:	n/a	chr6:30949880-30949893
9	STAT3	chr6:30949635-30950228	MCF10A-Er-Src	breast:	n/a	chr6:30949972-30949981 chr6:30949973-30949982 chr6:30949971-30949982
10	CTCF	chr6:30949640-30949790	GM12866	blood:	n/a	n/a
11	CTCF	chr6:30949660-30949810	HepG2	liver:	n/a	n/a
12	CTCF	chr6:30949620-30949770	HVMF	connective:	n/a	n/a
13	CTCF	chr6:30949660-30949810	GM12864	blood:	n/a	n/a
14	CTCF	chr6:30949660-30949810	HBMEC	blood vessel:	n/a	n/a
15	STAT3	chr6:30949656-30950198	MCF10A-Er-Src	breast:	n/a	chr6:30949972-30949981 chr6:30949973-30949982 chr6:30949971-30949982
16	RAD21	chr6:30949646-30949992	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr6:30949667-30950185	SK-N-SH_RA	brain:	n/a	n/a
18	CTCF	chr6:30949620-30949770	RPTEC	kidney:	n/a	n/a
19	SIN3AK20	chr6:30949637-30950074	SK-N-SH	brain:	n/a	n/a
20	CTCF	chr6:30949580-30949730	HFF-Myc	foreskin:	n/a	n/a
21	CTCF	chr6:30949660-30949810	AG09309	skin:	n/a	n/a
22	CTCF	chr6:30949660-30949810	HCT-116	colon:	n/a	n/a
23	TEAD4	chr6:30949541-30949972	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr6:30949600-30949750	HAc	cerebellar:	n/a	n/a
25	RAD21	chr6:30949605-30950015	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr6:30949577-30949931	H1-hESC	embryonic stem cell:	n/a	chr6:30949880-30949893
27	CTCF	chr6:30949600-30949750	NHDF-neo	bronchial:	n/a	n/a
28	CTCF	chr6:30949658-30949857	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30915992..30918182-chr6:30949634..30951324,2	K562	blood:
2	chr6:30949349..30950069-chr6:31010283..31011164,2	MCF-7	breast:

Variant related genes	Relation type
MUC21	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12661157	1.00[ASN][1000 genomes]
rs1625781	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1632857	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1632869	0.90[ASN][1000 genomes]
rs1634713	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1634718	1.00[ASN][1000 genomes]
rs1634719	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1634724	0.90[ASN][1000 genomes]
rs1634727	0.90[ASN][1000 genomes]
rs17189819	1.00[ASN][1000 genomes]
rs2394436	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394437	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894053	1.00[ASN][1000 genomes]
rs3095085	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095086	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3131931	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56240511	1.00[ASN][1000 genomes]
rs886403	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv462743	chr6:30905313-30957766	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv601483	chr6:30905313-30957766	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv462744	chr6:30920890-30955681	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv601484	chr6:30920890-30955681	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	esv3358044	chr6:30940552-31000175	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv1805090	chr6:30942284-30966453	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1023108	chr6:30944982-30990490	Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2517425	HIST1H2BM	cis	cerebellum	SCAN
rs2517425	OR2B6	cis	parietal	SCAN
rs2517425	ZNF391	cis	cerebellum	SCAN
rs2517425	ITPR3	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30932200-30949800	Weak transcription	Right Atrium	heart
2	chr6:30933000-30950200	Weak transcription	Gastric	stomach
3	chr6:30940600-30949800	Weak transcription	Esophagus	oesophagus
4	chr6:30943200-30949800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:30944200-30949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:30944400-30949800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:30945400-30949800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:30949200-30950400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:30949400-30949800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:30949400-30949800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr6:30949600-30949800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr6:30949600-30949800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr6:30949600-30949800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr6:30949600-30949800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:30949600-30949800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:30949600-30949800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:30949600-30949800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:30949600-30949800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:30949600-30949800	Enhancers	Fetal Heart	heart
20	chr6:30949600-30949800	Enhancers	Ovary	ovary
21	chr6:30949600-30949800	Enhancers	NH-A	brain
22	chr6:30949600-30949800	Enhancers	NHEK	skin
23	chr6:30949600-30950000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:30949600-30950000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:30949600-30950000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr6:30949600-30950200	Active TSS	NHDF-Ad	bronchial
27	chr6:30949600-30950400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:30949600-30950400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr6:30949600-30950400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:30949600-30950400	Enhancers	Liver	Liver
31	chr6:30949600-30950400	Flanking Active TSS	Fetal Kidney	kidney
32	chr6:30949600-30950400	Enhancers	Fetal Muscle Leg	muscle
33	chr6:30949600-30950400	Enhancers	Placenta	Placenta
34	chr6:30949600-30950400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
35	chr6:30949600-30950400	Flanking Active TSS	HMEC	breast
36	chr6:30949600-30950600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:30949600-30950600	Flanking Active TSS	Osteobl	bone
38	chr6:30949600-30950800	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr6:30949600-30951600	Enhancers	Stomach Mucosa	stomach

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