Variant report

Variant	rs3886807
Chromosome Location	chr8:4852649-4852650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr8:4851865-4852725	H1-hESC	embryonic stem cell:	n/a	n/a
2	CHD2	chr8:4852526-4852653	H1-hESC	embryonic stem cell:	n/a	n/a
3	SUZ12	chr8:4848594-4852688	NT2-D1	testis:	n/a	n/a
4	TAF1	chr8:4852488-4852765	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr8:4852371-4852759	H1-hESC	embryonic stem cell:	n/a	chr8:4852378-4852392
6	ZNF143	chr8:4852397-4852730	H1-hESC	embryonic stem cell:	n/a	n/a
7	SIN3A	chr8:4851813-4852727	H1-hESC	embryonic stem cell:	n/a	chr8:4851827-4851840 chr8:4851882-4851891
8	POLR2A	chr8:4850290-4852659	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr8:4851660-4852751	H1-neurons	neurons:	n/a	n/a
10	CTBP2	chr8:4851153-4852740	H1-hESC	embryonic stem cell:	n/a	n/a
11	USF2	chr8:4852335-4852656	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr8:4851742-4852756	H1-hESC	embryonic stem cell:	n/a	n/a
13	REST	chr8:4851478-4852668	H1-neurons	neurons:	n/a	chr8:4852251-4852269 chr8:4851896-4851914 chr8:4851827-4851840

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:4852624-4852674	U87	brain:	n/a
2	chr8:4852624-4852674	Jurkat	blood:	n/a
3	chr8:4852624-4852674	SKMC	muscle:	n/a
4	chr8:4852624-4852674	HIPEpiC	eye:	n/a
5	chr8:4852624-4852674	HCPEpiC	choroid plexus:	n/a
6	chr8:4852624-4852674	HAEpiC	amniotic membrane:	n/a
7	chr8:4852624-4852674	NH-A	brain:	n/a
8	chr8:4852624-4852674	HMEC	breast:	n/a
9	chr8:4852624-4852674	IMR90	lung:	fetal
10	chr8:4852624-4852674	T-47D	breast:	n/a
11	chr8:4852624-4852674	HRE	kidney:	n/a
12	chr8:4852624-4852674	MCF10A-Er-Src	breast:	n/a
13	chr8:4852624-4852674	HCF	heart:	n/a
14	chr8:4852624-4852674	HUVEC	blood vessel:	n/a
15	chr8:4852624-4852674	MCF-7	breast:	n/a
16	chr8:4852624-4852674	NT2-D1	testis:	n/a
17	chr8:4852624-4852674	PANC-1	pancreas:	n/a
18	chr8:4852624-4852674	SK-N-SH	brain:	n/a
19	chr8:4852624-4852674	BE2_C	brain:	n/a
20	chr8:4852624-4852674	BJ	skin:	n/a
21	chr8:4852624-4852674	GM19239	blood:	n/a
22	chr8:4852624-4852674	SK-N-SH_RA	brain:	n/a
23	chr8:4852624-4852674	AG04450	lung:	fetal
24	chr8:4852624-4852674	HPAEpiC	pulmonary alveolar:	n/a
25	chr8:4852624-4852674	HepG2	liver:	n/a
26	chr8:4852624-4852674	AG04449	skin:	fetal
27	chr8:4852624-4852674	LNCaP	prostate:	n/a
28	chr8:4852624-4852674	PrEC	prostate:	n/a
29	chr8:4852624-4852674	ECC-1	luminal epithelium:	n/a
30	chr8:4852624-4852674	A549	lung:	n/a
31	chr8:4852624-4852674	SK-N-MC	brain:	n/a
32	chr8:4852624-4852674	PFSK-1	brain:	n/a
33	chr8:4852624-4852674	GM06990	blood:	n/a
34	chr8:4852624-4852674	Hela-S3	cervix:	n/a
35	chr8:4852624-4852674	HNPCEpiC	eye:	n/a
36	chr8:4852624-4852674	HCM	heart:	n/a
37	chr8:4852624-4852674	NHBE	bronchial:	n/a
38	chr8:4852624-4852674	AG09319	gingival:	n/a
39	chr8:4852624-4852674	ovcar-3	ovarian:	n/a
40	chr8:4852624-4852674	RPTEC	kidney:	n/a
41	chr8:4852624-4852674	HCT-116	colon:	n/a
42	chr8:4852624-4852674	GM12892	blood:	n/a
43	chr8:4852624-4852674	AoSMC	blood vessel:	n/a
44	chr8:4852624-4852674	Hepatocyte	liver:	n/a
45	chr8:4852624-4852674	NB4	blood:	n/a
46	chr8:4852624-4852674	GM12891	blood:	n/a
47	chr8:4852624-4852674	CMK	blood:	n/a
48	chr8:4852624-4852674	NHDF-neo	bronchial:	n/a
49	chr8:4852624-4852674	HRPEpiC	eye:	n/a
50	chr8:4852624-4852674	K562	blood:	n/a

No data

Variant related genes	Relation type
CSMD1	TF binding region
CSMD1	CpG island

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11776188	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3860870	0.85[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv609876	chr8:4494811-5092970	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1029480	chr8:4497596-5081032	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv498130	chr8:4532988-5176376	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1031026	chr8:4771072-5054326	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3886807	CSMD1	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:4848600-4852800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr8:4848600-4852800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
3	chr8:4848800-4852800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr8:4848800-4852800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr8:4850400-4852800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr8:4851000-4852800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr8:4851000-4852800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr8:4851200-4852800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr8:4851200-4852800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
10	chr8:4851200-4852800	Bivalent/Poised TSS	Fetal Brain Female	brain
11	chr8:4851400-4852800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr8:4851400-4852800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr8:4851400-4852800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr8:4851400-4852800	Active TSS	Brain Angular Gyrus	brain
15	chr8:4851400-4852800	Active TSS	Brain Anterior Caudate	brain
16	chr8:4851600-4852800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr8:4852000-4852800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr8:4852000-4852800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr8:4852000-4852800	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr8:4852000-4852800	Bivalent Enhancer	Liver	Liver
21	chr8:4852200-4852800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:4852200-4852800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
23	chr8:4852200-4853400	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr8:4852400-4852800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
25	chr8:4852400-4852800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
26	chr8:4852400-4853000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr8:4852600-4852800	Enhancers	Esophagus	oesophagus
28	chr8:4852600-4852800	Bivalent Enhancer	Fetal Heart	heart
29	chr8:4852600-4852800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr8:4852600-4853000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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