Variant report

Variant	rs7840386
Chromosome Location	chr8:120653842-120653843
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	RAD21	chr8:120653695-120653948	HepG2	liver:	n/a	chr8:120653802-120653812 chr8:120653800-120653812
2	CTCF	chr8:120653691-120653903	A549	lung:	n/a	n/a
3	CTCF	chr8:120653700-120653850	GM12874	blood:	n/a	n/a
4	CTCF	chr8:120653720-120653870	NHEK	skin:	n/a	n/a
5	CTCF	chr8:120653737-120653894	Gliobla	brain:	n/a	n/a
6	CTCF	chr8:120653740-120653890	HMF	breast:	n/a	n/a
7	CTCF	chr8:120653720-120653870	AG10803	skin:	n/a	n/a
8	CTCF	chr8:120653706-120653900	HUVEC	blood vessel:	n/a	n/a
9	NR2F2	chr8:120653711-120654257	MCF-7	breast:	n/a	n/a
10	CTCF	chr8:120653760-120653910	HepG2	liver:	n/a	n/a
11	CTCF	chr8:120653740-120653890	GM12865	blood:	n/a	n/a
12	CTCF	chr8:120653712-120653917	MCF-7	breast:	n/a	n/a
13	RAD21	chr8:120653623-120653977	H1-hESC	embryonic stem cell:	n/a	chr8:120653802-120653812 chr8:120653800-120653812
14	CTCF	chr8:120653740-120653890	HPAF	blood vessel:	n/a	n/a
15	CTCF	chr8:120653720-120653870	BE2_C	brain:	n/a	n/a
16	CTCF	chr8:120653760-120653910	GM12872	blood:	n/a	n/a
17	CTCF	chr8:120653720-120653870	NB4	blood:	n/a	n/a
18	SIN3AK20	chr8:120653719-120654351	MCF-7	breast:	n/a	n/a
19	CTCF	chr8:120653700-120653850	HepG2	liver:	n/a	n/a
20	CTCF	chr8:120653725-120653884	LNCaP	prostate:	n/a	n/a
21	CEBPB	chr8:120653705-120654161	Hela-S3	cervix:	n/a	n/a
22	CTCF	chr8:120653720-120653870	SAEC	small airway:	n/a	n/a
23	CTCF	chr8:120653760-120653910	HUVEC	blood vessel:	n/a	n/a
24	CTCF	chr8:120653748-120653877	MCF-7	breast:	n/a	n/a
25	CTCF	chr8:120653720-120653870	GM12869	blood:	n/a	n/a
26	CTCF	chr8:120653720-120653870	HVMF	connective:	n/a	n/a
27	CTCF	chr8:120653700-120653850	GM12864	blood:	n/a	n/a
28	CTCF	chr8:120653720-120653870	AG09319	gingival:	n/a	n/a
29	RUNX3	chr8:120653671-120654535	GM12878	blood:	n/a	n/a
30	CTCF	chr8:120653740-120653890	HEEpiC	esophagus:	n/a	n/a
31	CTCF	chr8:120653740-120653890	GM06990	blood:	n/a	n/a
32	CTCF	chr8:120653820-120653970	HBMEC	blood vessel:	n/a	n/a
33	CTCF	chr8:120653740-120653890	HAc	cerebellar:	n/a	n/a
34	SMC3	chr8:120653629-120654006	GM12878	blood:	n/a	chr8:120653802-120653812
35	GATA3	chr8:120653561-120654423	SK-N-SH	brain:	n/a	chr8:120654071-120654079 chr8:120654050-120654058 chr8:120654051-120654058 chr8:120654048-120654060 chr8:120654051-120654061 chr8:120654049-120654059 chr8:120654051-120654058 chr8:120654051-120654058
36	CTCF	chr8:120653800-120653950	HFF-Myc	foreskin:	n/a	n/a
37	RAD21	chr8:120653625-120654011	ECC-1	luminal epithelium:	n/a	chr8:120653802-120653812 chr8:120653800-120653812
38	CTCF	chr8:120653840-120653990	GM12865	blood:	n/a	n/a
39	STAT3	chr8:120653576-120654071	MCF10A-Er-Src	breast:	n/a	n/a
40	TCF7L2	chr8:120653753-120654205	Hela-S3	cervix:	n/a	chr8:120654032-120654048 chr8:120654032-120654048
41	CTCF	chr8:120653614-120654046	HCT-116	colon:	n/a	n/a
42	CTCF	chr8:120653700-120653850	BJ	skin:	n/a	n/a
43	CTCF	chr8:120653740-120653890	HBMEC	blood vessel:	n/a	n/a
44	CTCF	chr8:120653720-120653870	GM12872	blood:	n/a	n/a
45	FOS	chr8:120653681-120653862	MCF10A-Er-Src	breast:	n/a	n/a
46	GATA2	chr8:120653694-120654407	SH-SY5Y	brain:	n/a	chr8:120654051-120654058 chr8:120654048-120654060 chr8:120654051-120654061 chr8:120654049-120654059 chr8:120654051-120654058 chr8:120654051-120654058
47	CTCF	chr8:120653760-120653910	GM12870	blood:	n/a	n/a
48	CTCF	chr8:120653780-120653930	GM12871	blood:	n/a	n/a
49	WRNIP1	chr8:120653836-120654102	GM12878	blood:	n/a	n/a
50	TCF7L2	chr8:120653682-120654379	HEK293	kidney:	n/a	chr8:120654032-120654048 chr8:120654032-120654048

No.	Distal block	Cell Line	Cell type
1	chr8:120521567..120522594-chr8:120653329..120654356,13	MCF-7	breast:
2	chr8:120653727..120654418-chr8:120667067..120667872,2	MCF-7	breast:
3	chr8:120464324..120466274-chr8:120652065..120654890,2	MCF-7	breast:
4	chr8:120521783..120522581-chr8:120653430..120654567,4	MCF-7	breast:
5	chr8:120463850..120464593-chr8:120653375..120654451,5	MCF-7	breast:

Variant related genes	Relation type
ENPP2	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11775668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11778951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11786983	1.00[CEU][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16892900	0.82[CHD][hapmap]
rs4871419	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4871420	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58361300	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59168593	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6469837	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6984417	0.89[ASN][1000 genomes]
rs6989212	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6996637	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6996969	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7014683	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7837894	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7839329	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs965301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv868916	chr8:119911943-120762250	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv534028	chr8:120348940-120906079	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv949368	chr8:120568034-121019872	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1021071	chr8:120589963-120968317	Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv465789	chr8:120636850-120994394	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv612111	chr8:120636850-120994394	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv427826	chr8:120642181-120953395	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7840386	DSCC1	cis	parietal	SCAN
rs7840386	UTP23	cis	parietal	SCAN
rs7840386	ENPP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120651400-120656000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:120651800-120656800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr8:120651800-120657400	Weak transcription	Placenta	Placenta
4	chr8:120651800-120667600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr8:120652000-120654000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr8:120652000-120654600	Enhancers	Brain Cingulate Gyrus	brain
7	chr8:120652000-120656600	Enhancers	Fetal Lung	lung
8	chr8:120652200-120654200	Enhancers	Brain Anterior Caudate	brain
9	chr8:120652200-120654400	Enhancers	Adipose Nuclei	Adipose
10	chr8:120652200-120655200	Enhancers	Primary hematopoietic stem cells	blood
11	chr8:120652200-120656600	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr8:120652200-120657400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr8:120652200-120657600	Enhancers	Brain Substantia Nigra	brain
14	chr8:120652400-120654000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr8:120652400-120654400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr8:120652400-120655200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr8:120652400-120655400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr8:120652400-120655600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:120652400-120655600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr8:120652400-120655800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr8:120652400-120655800	Weak transcription	Brain Angular Gyrus	brain
22	chr8:120652400-120656400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr8:120652600-120654000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr8:120652600-120657200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr8:120652800-120655600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr8:120653000-120656600	Enhancers	Brain Hippocampus Middle	brain
27	chr8:120653200-120654400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr8:120653400-120654400	Enhancers	Duodenum Mucosa	Duodenum
29	chr8:120653400-120657800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr8:120653600-120654200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr8:120653600-120654400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr8:120653600-120655800	Enhancers	Primary T cells from cord blood	blood
33	chr8:120653800-120654000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr8:120653800-120654000	Enhancers	Small Intestine	intestine
35	chr8:120653800-120654200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr8:120653800-120654200	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr8:120653800-120654200	Enhancers	Fetal Thymus	thymus
38	chr8:120653800-120654200	Flanking Active TSS	GM12878-XiMat	blood
39	chr8:120653800-120654200	Enhancers	Hela-S3	cervix
40	chr8:120653800-120654600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr8:120653800-120655000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr8:120653800-120655000	Enhancers	Primary B cells from cord blood	blood
43	chr8:120653800-120655000	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr8:120653800-120655000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr8:120653800-120655000	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr8:120653800-120655400	Enhancers	Primary B cells from peripheral blood	blood

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