Variant report

Variant	rs3814463
Chromosome Location	chr7:119912849-119912850
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	MTA3	chr7:119912097-119913263	GM12878	blood:	n/a	n/a
2	SPI1	chr7:119912626-119913012	GM12891	blood:	n/a	n/a
3	POLR2A	chr7:119912042-119914649	GM12891	blood:	n/a	n/a
4	WRNIP1	chr7:119912311-119913043	GM12878	blood:	n/a	n/a
5	CTCF	chr7:119912840-119912990	NHEK	skin:	n/a	n/a
6	CTCF	chr7:119912840-119912990	GM06990	blood:	n/a	n/a
7	CTCF	chr7:119912700-119912850	GM12870	blood:	n/a	n/a
8	CTCF	chr7:119911830-119912849	A549	lung:	n/a	chr7:119912406-119912427 chr7:119912412-119912428 chr7:119912416-119912424 chr7:119912411-119912429
9	E2F6	chr7:119912756-119913242	H1-hESC	embryonic stem cell:	n/a	chr7:119913176-119913185
10	MXI1	chr7:119912318-119913120	GM12878	blood:	n/a	n/a
11	POLR2A	chr7:119912751-119914145	GM19099	blood:	n/a	n/a
12	ELF1	chr7:119912787-119913446	GM12878	blood:	n/a	chr7:119912815-119912826
13	POLR2A	chr7:119912285-119914624	GM12878	blood:	n/a	n/a
14	SPI1	chr7:119912653-119912972	GM12891	blood:	n/a	n/a
15	MAX	chr7:119912710-119913285	H1-hESC	embryonic stem cell:	n/a	chr7:119913174-119913184
16	CTCF	chr7:119912720-119912870	NHLF	lung:	n/a	n/a
17	SPI1	chr7:119912632-119913056	GM12878	blood:	n/a	n/a
18	MAX	chr7:119912835-119913299	ECC-1	luminal epithelium:	n/a	chr7:119913174-119913184
19	CTCF	chr7:119912840-119912990	K562	blood:	n/a	n/a
20	CTCF	chr7:119912800-119912950	GM12874	blood:	n/a	n/a
21	ZNF143	chr7:119912264-119913112	H1-hESC	embryonic stem cell:	n/a	n/a
22	SPI1	chr7:119912557-119913098	HL-60	blood:	n/a	n/a
23	ZEB1	chr7:119912805-119913371	GM12878	blood:	n/a	n/a
24	CHD1	chr7:119912462-119912946	H1-hESC	embryonic stem cell:	n/a	n/a
25	MYC	chr7:119912614-119913120	H1-hESC	embryonic stem cell:	n/a	n/a
26	RUNX3	chr7:119912717-119913204	GM12878	blood:	n/a	n/a
27	CTBP2	chr7:119912499-119913239	H1-hESC	embryonic stem cell:	n/a	n/a
28	BACH1	chr7:119912779-119913276	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr7:119912840-119912990	BJ	skin:	n/a	n/a
30	PML	chr7:119912156-119914442	GM12878	blood:	n/a	chr7:119913738-119913746
31	TAF1	chr7:119912729-119913247	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr7:119912465-119914229	GM19193	blood:	n/a	n/a
33	RUNX3	chr7:119912690-119913288	GM12878	blood:	n/a	n/a
34	POLR2A	chr7:119912297-119914489	GM18505	blood:	n/a	n/a
35	HDAC2	chr7:119912575-119913202	H1-hESC	embryonic stem cell:	n/a	chr7:119913193-119913201 chr7:119912815-119912829
36	TEAD4	chr7:119912699-119913091	H1-hESC	embryonic stem cell:	n/a	n/a
37	E2F6	chr7:119912664-119913395	H1-hESC	embryonic stem cell:	n/a	chr7:119913360-119913372 chr7:119913176-119913185 chr7:119913365-119913374
38	MAZ	chr7:119912212-119913267	GM12878	blood:	n/a	chr7:119913174-119913184
39	CHD1	chr7:119912396-119913017	GM12878	blood:	n/a	n/a
40	CTCF	chr7:119912195-119913075	GM12878	blood:	n/a	chr7:119912406-119912427 chr7:119912412-119912428 chr7:119912416-119912424 chr7:119912411-119912429
41	CTCF	chr7:119912760-119912910	GM12872	blood:	n/a	n/a
42	SIN3A	chr7:119912256-119914387	H1-hESC	embryonic stem cell:	n/a	n/a
43	FOXM1	chr7:119912158-119913187	GM12878	blood:	n/a	n/a
44	RAD21	chr7:119912126-119913106	H1-hESC	embryonic stem cell:	n/a	chr7:119912419-119912426 chr7:119912412-119912424 chr7:119912409-119912428 chr7:119912413-119912427
45	POLR2A	chr7:119912823-119914077	H1-neurons	neurons:	n/a	n/a
46	SP1	chr7:119912704-119913137	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAX	chr7:119912705-119913286	H1-hESC	embryonic stem cell:	n/a	chr7:119913174-119913184
48	POLR2A	chr7:119912750-119913318	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr7:119911907-119912907	SK-N-SH	brain:	n/a	chr7:119912406-119912427 chr7:119912412-119912428 chr7:119912416-119912424 chr7:119912411-119912429
50	POLR2A	chr7:119912786-119914131	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
KCND2	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10224017	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224700	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10224809	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10237275	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10247464	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10250387	0.89[ASN][1000 genomes]
rs10251877	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10252729	0.84[ASN][1000 genomes]
rs10278455	0.84[ASN][1000 genomes]
rs10279729	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1035014	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10488287	0.83[ASN][1000 genomes]
rs10953908	0.83[ASN][1000 genomes]
rs11487122	0.95[EUR][1000 genomes]
rs11768610	0.86[EUR][1000 genomes]
rs12533932	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12666459	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12706276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12706279	0.82[ASN][1000 genomes]
rs12706280	0.83[ASN][1000 genomes]
rs1304206	0.83[ASN][1000 genomes]
rs17142555	0.82[EUR][1000 genomes]
rs17142585	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17594101	0.96[EUR][1000 genomes]
rs17594220	0.96[EUR][1000 genomes]
rs1860704	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1990429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2107994	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2190183	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2191734	0.98[ASN][1000 genomes]
rs2191736	0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs2191737	0.83[ASN][1000 genomes]
rs2402525	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2402526	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2402527	0.83[ASN][1000 genomes]
rs28532220	0.82[EUR][1000 genomes]
rs3735339	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4730954	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[ASN][1000 genomes]
rs4730955	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4730956	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4730958	0.83[ASN][1000 genomes]
rs4730960	0.83[ASN][1000 genomes]
rs55963403	0.95[EUR][1000 genomes]
rs56244901	0.96[EUR][1000 genomes]
rs62469503	0.95[EUR][1000 genomes]
rs62469505	0.95[EUR][1000 genomes]
rs62469506	0.96[EUR][1000 genomes]
rs62469507	0.96[EUR][1000 genomes]
rs6466739	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6466740	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6466741	0.98[ASN][1000 genomes]
rs6942715	0.83[ASN][1000 genomes]
rs6943223	0.88[ASN][1000 genomes]
rs6956408	0.82[EUR][1000 genomes]
rs6956570	0.82[EUR][1000 genomes]
rs6956643	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6969916	0.94[EUR][1000 genomes]
rs6973947	0.81[EUR][1000 genomes]
rs6974349	0.84[ASN][1000 genomes]
rs6978586	0.95[EUR][1000 genomes]
rs73213458	0.95[EUR][1000 genomes]
rs7782622	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7790816	0.87[CHD][hapmap]
rs7792688	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7792980	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[ASN][1000 genomes]
rs7795487	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7801487	0.91[ASN][1000 genomes]
rs7805413	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8180795	0.83[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	nsv608326	chr7:119828331-119995890	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv1843078	chr7:119909603-119934006	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3814463	CADPS2	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:119911400-119914800	Active TSS	Brain Anterior Caudate	brain
2	chr7:119911600-119914400	Active TSS	Brain Angular Gyrus	brain
3	chr7:119912000-119914000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr7:119912000-119914400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:119912000-119914600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr7:119912000-119914600	Active TSS	Fetal Brain Male	brain
7	chr7:119912000-119914600	Active TSS	GM12878-XiMat	blood
8	chr7:119912000-119914800	Active TSS	Brain Substantia Nigra	brain
9	chr7:119912200-119914000	Active TSS	Fetal Brain Female	brain
10	chr7:119912200-119914000	Bivalent/Poised TSS	Fetal Lung	lung
11	chr7:119912200-119914200	Active TSS	Fetal Kidney	kidney
12	chr7:119912200-119914400	Active TSS	Brain Hippocampus Middle	brain
13	chr7:119912200-119914600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:119912200-119914600	Active TSS	Ovary	ovary
15	chr7:119912200-119914800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:119912400-119913000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr7:119912400-119913000	Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr7:119912400-119913200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
19	chr7:119912400-119913200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:119912400-119913200	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr7:119912400-119913200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
22	chr7:119912400-119913200	Flanking Bivalent TSS/Enh	HMEC	breast
23	chr7:119912400-119913200	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
24	chr7:119912400-119913400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:119912400-119913400	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr7:119912400-119913600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr7:119912400-119913600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:119912400-119913600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr7:119912400-119913600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:119912400-119913600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:119912400-119913600	Active TSS	Aorta	Aorta
32	chr7:119912400-119913600	Bivalent Enhancer	Liver	Liver
33	chr7:119912400-119913600	Active TSS	NHDF-Ad	bronchial
34	chr7:119912400-119913600	Active TSS	NHLF	lung
35	chr7:119912400-119913800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:119912400-119913800	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr7:119912400-119913800	Active TSS	Fetal Heart	heart
38	chr7:119912400-119913800	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr7:119912400-119914000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr7:119912400-119914000	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr7:119912400-119914000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr7:119912400-119914000	Active TSS	Duodenum Mucosa	Duodenum
43	chr7:119912400-119914000	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr7:119912400-119914000	Active TSS	Psoas Muscle	Psoas
45	chr7:119912400-119914000	Bivalent/Poised TSS	Right Ventricle	heart
46	chr7:119912400-119914000	Bivalent/Poised TSS	HSMM	muscle
47	chr7:119912400-119914000	Bivalent/Poised TSS	HSMMtube	muscle
48	chr7:119912400-119914200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr7:119912400-119914200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr7:119912400-119914200	Active TSS	Muscle Satellite Cultured Cells	--

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