Variant report

Variant	rs1513524
Chromosome Location	chr8:114450518-114450519
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	CTCF	chr8:114450319-114450538	GM19239	blood:	n/a	n/a
2	KAP1	chr8:114449958-114451181	HEK293	kidney:	n/a	n/a
3	RAD21	chr8:114449853-114451074	H1-hESC	embryonic stem cell:	n/a	chr8:114450100-114450114 chr8:114450328-114450340 chr8:114450096-114450115
4	ZNF143	chr8:114449914-114450534	Hela-S3	cervix:	n/a	n/a
5	TCF7L2	chr8:114449803-114450679	Hela-S3	cervix:	n/a	n/a
6	FOXP2	chr8:114450008-114450653	PFSK-1	brain:	n/a	n/a
7	ZKSCAN1	chr8:114449992-114450541	Hela-S3	cervix:	n/a	n/a
8	SMC3	chr8:114449889-114450615	GM12878	blood:	n/a	chr8:114450100-114450114
9	CEBPB	chr8:114449885-114450607	MCF-7	breast:	n/a	chr8:114450076-114450087 chr8:114450095-114450106
10	CTCF	chr8:114450480-114450630	GM12867	blood:	n/a	n/a
11	CTCF	chr8:114450480-114450630	HMF	breast:	n/a	n/a
12	POLR2A	chr8:114449877-114450547	H1-neurons	neurons:	n/a	n/a
13	RAD21	chr8:114449814-114450638	MCF-7	breast:	n/a	chr8:114450100-114450114 chr8:114450328-114450340 chr8:114450096-114450115
14	SMC3	chr8:114449759-114450919	SK-N-SH	brain:	n/a	chr8:114450100-114450114
15	CEBPB	chr8:114449904-114450521	Hela-S3	cervix:	n/a	chr8:114450076-114450087 chr8:114450095-114450106
16	RAD21	chr8:114449649-114451222	SK-N-SH	brain:	n/a	chr8:114450100-114450114 chr8:114450328-114450340 chr8:114450096-114450115
17	MAZ	chr8:114449984-114450570	Hela-S3	cervix:	n/a	n/a
18	RAD21	chr8:114449751-114450585	MCF-7	breast:	n/a	chr8:114450100-114450114 chr8:114450328-114450340 chr8:114450096-114450115
19	TFAP2A	chr8:114450013-114451057	Hela-S3	cervix:	n/a	chr8:114450395-114450405 chr8:114450395-114450405 chr8:114450393-114450407 chr8:114451010-114451021 chr8:114450395-114450405 chr8:114451010-114451021 chr8:114451010-114451021 chr8:114450393-114450407 chr8:114451010-114451021 chr8:114450391-114450406 chr8:114450395-114450405 chr8:114450393-114450407 chr8:114450393-114450407
20	CTCF	chr8:114449972-114450643	GM12891	blood:	n/a	chr8:114450099-114450115 chr8:114450098-114450116 chr8:114450093-114450114 chr8:114450100-114450113
21	POLR2A	chr8:114450450-114450786	MCF-7	breast:	n/a	n/a
22	SMC3	chr8:114449701-114450615	Hela-S3	cervix:	n/a	chr8:114450100-114450114
23	CTCF	chr8:114449876-114450544	GM12878	blood:	n/a	chr8:114450099-114450115 chr8:114450098-114450116 chr8:114450093-114450114 chr8:114450100-114450113
24	CTCF	chr8:114449631-114450715	SK-N-SH	brain:	n/a	chr8:114450099-114450115 chr8:114450098-114450116 chr8:114450093-114450114 chr8:114450100-114450113
25	ZNF143	chr8:114449940-114450703	H1-hESC	embryonic stem cell:	n/a	n/a
26	SUZ12	chr8:114449932-114451284	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr8:114450474-114450554	MCF-7	breast:	n/a	n/a
28	POLR2A	chr8:114450518-114450522	MCF-7	breast:	n/a	n/a
29	TFAP2C	chr8:114449991-114451182	Hela-S3	cervix:	n/a	chr8:114450391-114450406
30	CTCF	chr8:114450480-114450630	SAEC	small airway:	n/a	n/a
31	HA-E2F1	chr8:114449826-114451240	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
CSMD3	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10089887	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11786058	0.82[EUR][1000 genomes]
rs11985886	0.80[EUR][1000 genomes]
rs12541897	0.80[EUR][1000 genomes]
rs12545155	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12676699	0.84[EUR][1000 genomes]
rs12678354	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1382467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1513515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1513523	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1551957	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28696718	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2927865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2927868	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2927869	1.00[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2927870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2927871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2927872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2927873	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2927874	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2942835	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2942845	0.85[EUR][1000 genomes]
rs2942848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2942851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2942852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2942853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2954881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954894	0.85[EUR][1000 genomes]
rs4311682	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4354335	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4531082	0.89[CEU][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4593574	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6469455	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6469457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7002354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7003686	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7829130	0.82[EUR][1000 genomes]
rs7831822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7839252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7839352	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9297493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9643079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9649937	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs966371	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv817379	chr8:114338391-115011632	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2754463	chr8:114353649-114501547	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2761461	chr8:114420164-114462173	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831429	chr8:114438561-114595565	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1513524	CSMD3	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:114444200-114450800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr8:114444400-114450600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
3	chr8:114446400-114450600	Active TSS	Brain Anterior Caudate	brain
4	chr8:114446400-114451200	Active TSS	Brain Angular Gyrus	brain
5	chr8:114446600-114450600	Active TSS	Brain Germinal Matrix	brain
6	chr8:114447000-114450800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
7	chr8:114448400-114450600	Active TSS	Fetal Brain Male	brain
8	chr8:114448800-114450800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:114448800-114450800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr8:114448800-114450800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
11	chr8:114448800-114451000	Bivalent/Poised TSS	Fetal Kidney	kidney
12	chr8:114448800-114451200	Active TSS	Brain Cingulate Gyrus	brain
13	chr8:114449000-114451000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr8:114449200-114450800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
15	chr8:114449200-114451000	Bivalent Enhancer	Fetal Heart	heart
16	chr8:114449400-114450600	Enhancers	Spleen	Spleen
17	chr8:114449400-114450800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr8:114449600-114450600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr8:114449600-114450600	Bivalent Enhancer	Liver	Liver
20	chr8:114449600-114450800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr8:114449600-114450800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr8:114449600-114450800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
23	chr8:114449600-114450800	Flanking Bivalent TSS/Enh	NH-A	brain
24	chr8:114449600-114451000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr8:114449800-114450600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
26	chr8:114449800-114450600	Active TSS	Psoas Muscle	Psoas
27	chr8:114449800-114450600	Active TSS	Hela-S3	cervix
28	chr8:114449800-114451000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr8:114449800-114451000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr8:114449800-114451000	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr8:114449800-114451200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr8:114449800-114451200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr8:114450000-114450600	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr8:114450000-114450600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
35	chr8:114450000-114450800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr8:114450000-114450800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr8:114450000-114450800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
38	chr8:114450000-114451000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
39	chr8:114450000-114451000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr8:114450000-114451200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr8:114450000-114451200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
42	chr8:114450000-114451200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr8:114450200-114450600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr8:114450200-114450600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
45	chr8:114450200-114450600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr8:114450200-114450600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
47	chr8:114450200-114450600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
48	chr8:114450200-114450600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
49	chr8:114450200-114450600	Bivalent Enhancer	Fetal Thymus	thymus
50	chr8:114450200-114450600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum

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