Variant report

Variant	rs3130100
Chromosome Location	chr6:33283766-33283767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr6:33279967-33283766	IMR90	lung:	n/a	n/a
2	POLR2A	chr6:33283008-33283816	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:33280382-33283827	K562	blood:	n/a	n/a
4	ZNF263	chr6:33283536-33283802	HEK293-T-REx	kidney:	n/a	n/a
5	POLR2A	chr6:33280837-33284738	K562	blood:	n/a	n/a
6	POLR2A	chr6:33280219-33284024	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr6:33279940-33283845	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33283215..33284795-chr6:33393304..33395284,2	MCF-7	breast:
2	chr6:33238090..33243099-chr6:33279379..33286881,12	MCF-7	breast:
3	chr6:33282976..33285043-chr6:33316013..33318058,2	K562	blood:
4	chr6:33280908..33284579-chr6:33359142..33361187,5	K562	blood:
5	chr6:33259755..33275794-chr6:33276314..33291745,68	MCF-7	breast:
6	chr6:33283728..33287391-chr6:33357794..33361686,6	MCF-7	breast:
7	chr6:33280795..33292485-chr6:33374786..33387605,31	K562	blood:
8	chr6:33282784..33285441-chr6:33377826..33380385,3	MCF-7	breast:
9	chr6:33256218..33259091-chr6:33279064..33284854,6	MCF-7	breast:
10	chr6:33283316..33288344-chr6:33357863..33362367,8	K562	blood:
11	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:

No data

Variant related genes	Relation type
TAPBP	TF binding region
ENSG00000227057	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000204220	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000223501	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1014779	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1061783	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800838	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2013891	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2071888	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2071889	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2395379	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2894334	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3106190	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3106195	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130016	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3130018	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3130099	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130101	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130262	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130263	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130264	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130265	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3130266	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130267	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3130269	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3130270	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3130271	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3135405	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3135407	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3135408	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3135409	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs446735	0.80[EUR][1000 genomes]
rs456261	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs463260	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs464865	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9277968	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3130100	C6orf10	cis	normal skin	skin_eQTL
rs3130100	TAPBP	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33282200-33284600	Weak transcription	Small Intestine	intestine
2	chr6:33282400-33283800	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr6:33282600-33283800	Enhancers	Gastric	stomach
4	chr6:33282600-33284800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:33282600-33285000	Weak transcription	Aorta	Aorta
6	chr6:33282600-33285000	Enhancers	Fetal Heart	heart
7	chr6:33282600-33285000	Weak transcription	Ovary	ovary
8	chr6:33282800-33283800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:33282800-33283800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:33282800-33284000	Enhancers	Fetal Muscle Leg	muscle
11	chr6:33282800-33284400	Enhancers	Dnd41	blood
12	chr6:33282800-33284600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:33282800-33284600	Weak transcription	Brain Substantia Nigra	brain
14	chr6:33282800-33284800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:33282800-33284800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:33282800-33284800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:33282800-33284800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:33282800-33284800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr6:33282800-33284800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr6:33282800-33285000	Enhancers	Right Atrium	heart
21	chr6:33282800-33285400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:33283000-33283800	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:33283000-33284200	Weak transcription	Brain Angular Gyrus	brain
24	chr6:33283000-33284400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:33283000-33284400	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:33283000-33284400	Weak transcription	Brain Anterior Caudate	brain
27	chr6:33283000-33284400	Genic enhancers	Spleen	Spleen
28	chr6:33283000-33284600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:33283000-33284600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:33283000-33284600	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr6:33283000-33284800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:33283000-33284800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:33283000-33284800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:33283000-33284800	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr6:33283000-33284800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr6:33283000-33284800	Enhancers	Adipose Nuclei	Adipose
37	chr6:33283000-33284800	Weak transcription	HepG2	liver
38	chr6:33283000-33284800	Weak transcription	HSMMtube	muscle
39	chr6:33283000-33284800	Weak transcription	HUVEC	blood vessel
40	chr6:33283000-33285000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:33283000-33285000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr6:33283000-33285000	Genic enhancers	Fetal Stomach	stomach
43	chr6:33283200-33283800	Enhancers	Colonic Mucosa	Colon
44	chr6:33283200-33283800	Genic enhancers	Fetal Intestine Large	intestine
45	chr6:33283200-33284000	Enhancers	Primary hematopoietic stem cells	blood
46	chr6:33283200-33284000	Enhancers	Pancreas	Pancrea
47	chr6:33283200-33284000	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr6:33283200-33284000	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr6:33283200-33284000	Enhancers	K562	blood
50	chr6:33283200-33284200	Weak transcription	Brain Hippocampus Middle	brain

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