Variant report

Variant	rs17460940
Chromosome Location	chr6:128813085-128813086
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	FOXP2	chr6:128812895-128813175	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr6:128812807-128813166	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr6:128812753-128813404	U87	brain:	n/a	n/a
4	GATA3	chr6:128812124-128813339	SK-N-SH	brain:	n/a	chr6:128812463-128812472
5	MYC	chr6:128812893-128813372	MCF10A-Er-Src	breast:	n/a	n/a
6	EBF1	chr6:128812835-128813298	GM12878	blood:	n/a	chr6:128813066-128813075 chr6:128813064-128813075 chr6:128813064-128813077 chr6:128813065-128813075
7	KAP1	chr6:128812510-128813406	U2OS	brain:	n/a	n/a
8	POLR2A	chr6:128812690-128813492	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:128812795-128813383	PFSK-1	brain:	n/a	n/a
10	FOS	chr6:128813068-128813386	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr6:128812768-128813404	U87	brain:	n/a	n/a
12	CEBPB	chr6:128813053-128813399	IMR90	lung:	n/a	chr6:128813217-128813230
13	POLR2A	chr6:128812338-128813527	HUVEC	blood vessel:	n/a	n/a
14	GATA2	chr6:128812219-128813442	HUVEC	blood vessel:	n/a	chr6:128812463-128812472
15	POLR2A	chr6:128812213-128813276	MCF10A-Er-Src	breast:	n/a	n/a
16	EP300	chr6:128812725-128813103	SK-N-SH_RA	brain:	n/a	n/a
17	EBF1	chr6:128812870-128813234	GM12878	blood:	n/a	chr6:128813066-128813075 chr6:128813064-128813075 chr6:128813064-128813077 chr6:128813065-128813075
18	FOS	chr6:128813078-128813314	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128810906..128814817-chr6:128838628..128842024,3	MCF-7	breast:

Variant related genes	Relation type
PTPRK	TF binding region
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1012629	0.94[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10872331	1.00[CHD][hapmap]
rs11154439	1.00[CHD][hapmap]
rs11756545	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[ASN][1000 genomes]
rs17364020	1.00[CHD][hapmap]
rs17364090	1.00[CHD][hapmap]
rs17364118	1.00[CHD][hapmap]
rs17459694	0.94[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17460765	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17461178	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17461290	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17461370	1.00[CHD][hapmap]
rs1935130	0.94[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326702	1.00[CHD][hapmap]
rs55848328	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62425728	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425730	1.00[ASN][1000 genomes]
rs62425732	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425734	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425736	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9482886	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491959	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491965	0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs9492002	1.00[CHD][hapmap]
rs9492021	1.00[CHD][hapmap]

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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17460940	MOXD1	cis	parietal	SCAN
rs17460940	AKAP7	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128797400-128822000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:128808800-128830800	Weak transcription	Lung	lung
3	chr6:128811000-128814400	Enhancers	Small Intestine	intestine
4	chr6:128811400-128813400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr6:128811400-128813400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:128811400-128813800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:128811600-128813200	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr6:128811600-128814000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:128811800-128813400	Active TSS	Ovary	ovary
10	chr6:128811800-128813600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr6:128811800-128816600	Weak transcription	Gastric	stomach
12	chr6:128812000-128813200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:128812000-128814200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:128812000-128814200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:128812000-128817000	Genic enhancers	HepG2	liver
16	chr6:128812200-128813200	Active TSS	Brain Anterior Caudate	brain
17	chr6:128812200-128813200	Active TSS	Right Atrium	heart
18	chr6:128812200-128813400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:128812200-128813400	Flanking Active TSS	HUVEC	blood vessel
20	chr6:128812200-128813600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:128812200-128813600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr6:128812200-128813600	Flanking Active TSS	HMEC	breast
23	chr6:128812200-128814000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr6:128812200-128814200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr6:128812200-128815000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:128812200-128817200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr6:128812400-128813200	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr6:128812400-128813200	Active TSS	Brain Angular Gyrus	brain
29	chr6:128812400-128813200	Active TSS	Brain Hippocampus Middle	brain
30	chr6:128812400-128813200	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr6:128812400-128813200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:128812400-128813400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:128812400-128813400	Active TSS	Adipose Nuclei	Adipose
34	chr6:128812400-128813600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:128812400-128813600	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr6:128812400-128814200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr6:128812600-128813200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr6:128812600-128813200	Active TSS	Brain Substantia Nigra	brain
39	chr6:128812600-128813200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr6:128812600-128813200	Active TSS	Fetal Brain Male	brain
41	chr6:128812600-128813200	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr6:128812600-128813200	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr6:128812600-128813200	Active TSS	Right Ventricle	heart
44	chr6:128812600-128813200	Active TSS	HSMM	muscle
45	chr6:128812600-128813400	Enhancers	H9 Cell Line	embryonic stem cell
46	chr6:128812600-128813400	Active TSS	Colonic Mucosa	Colon
47	chr6:128812600-128813400	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr6:128812600-128813400	Active TSS	Left Ventricle	heart
49	chr6:128812600-128813400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr6:128812600-128813400	Active TSS	Rectal Smooth Muscle	rectum

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