Variant report

Variant	rs6960348
Chromosome Location	chr7:56124240-56124241
allele	A/G
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	chr7:56123827-56124312	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr7:56123860-56124346	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr7:56123835-56124364	HepG2	liver:	n/a	n/a
4	POLR2A	chr7:56124117-56124302	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
CCT6A	TF binding region
PSPH	TF binding region
SNORA15	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10265826	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10274148	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12154781	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12155441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12536548	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12537948	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12668193	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12668532	0.95[CEU][hapmap]
rs12671494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12673255	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13438048	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2014042	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242509	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2270244	0.94[CEU][hapmap]
rs28438587	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28558245	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3778867	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3813505	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4255091	0.87[CHB][hapmap]
rs4345511	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4424212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4427122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4496923	0.91[CHB][hapmap]
rs4585698	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55940597	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58251663	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59723101	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6947671	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6955639	0.95[CEU][hapmap]
rs6962857	0.90[CHB][hapmap]
rs6970842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6971804	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73140779	0.95[AFR][1000 genomes]
rs73140793	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73140794	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs766334	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7778601	0.95[CEU][hapmap]
rs7793536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7793614	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7804578	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription 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	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription 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	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6960348	SUMF2	cis	Esophagus Muscularis	GTEx
rs6960348	SUMF2	cis	Whole Blood	GTEx
rs6960348	SUMF2	cis	lung	GTEx
rs6960348	SUMF2	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56120200-56125600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:56120200-56131200	Weak transcription	Aorta	Aorta
3	chr7:56120600-56131000	Strong transcription	Adipose Nuclei	Adipose
4	chr7:56120800-56125200	Weak transcription	Colonic Mucosa	Colon
5	chr7:56120800-56127400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:56120800-56130000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr7:56120800-56130400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:56120800-56130800	Strong transcription	Brain Angular Gyrus	brain
9	chr7:56120800-56131200	Strong transcription	Fetal Thymus	thymus
10	chr7:56120800-56131400	Strong transcription	Fetal Muscle Leg	muscle
11	chr7:56120800-56131600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:56121000-56124800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:56121000-56130000	Weak transcription	Stomach Mucosa	stomach
14	chr7:56121000-56130800	Strong transcription	Fetal Lung	lung
15	chr7:56121000-56131000	Strong transcription	Brain Anterior Caudate	brain
16	chr7:56121000-56131200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr7:56121000-56131200	Strong transcription	Brain Hippocampus Middle	brain
18	chr7:56121200-56126000	Strong transcription	Colon Smooth Muscle	Colon
19	chr7:56121200-56128600	Strong transcription	HSMMtube	muscle
20	chr7:56121200-56129400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr7:56121200-56129400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr7:56121200-56129400	Strong transcription	Osteobl	bone
23	chr7:56121200-56130400	Strong transcription	Liver	Liver
24	chr7:56121200-56130600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr7:56121200-56130800	Strong transcription	Brain Cingulate Gyrus	brain
26	chr7:56121200-56130800	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr7:56121200-56131200	Strong transcription	Brain Germinal Matrix	brain
28	chr7:56121200-56131200	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr7:56121200-56131400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr7:56121200-56131400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr7:56121400-56125000	Weak transcription	Pancreas	Pancrea
32	chr7:56121400-56125400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr7:56121400-56126000	Strong transcription	Fetal Kidney	kidney
34	chr7:56121400-56128000	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr7:56121400-56128000	Strong transcription	HSMM	muscle
36	chr7:56121400-56128400	Strong transcription	NH-A	brain
37	chr7:56121400-56129000	Genic enhancers	HepG2	liver
38	chr7:56121400-56129400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr7:56121400-56129800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr7:56121400-56130600	Strong transcription	Primary B cells from peripheral blood	blood
41	chr7:56121400-56130800	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr7:56121400-56130800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr7:56121400-56130800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr7:56121400-56131000	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr7:56121400-56131000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:56121400-56131000	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr7:56121400-56131200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr7:56121400-56131200	Strong transcription	Placenta	Placenta
49	chr7:56121400-56131200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr7:56121400-56131200	Genic enhancers	Dnd41	blood

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