Variant report

Variant	rs3818598
Chromosome Location	chr9:108210300-108210301
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	POLR2A	chr9:108209926-108211196	Hela-S3	cervix:	n/a	n/a
2	UBTF	chr9:108209988-108211263	K562	blood:	n/a	n/a
3	POLR2A	chr9:108209980-108210542	HepG2	liver:	n/a	n/a
4	ZNF143	chr9:108209820-108210447	GM12878	blood:	n/a	n/a
5	CHD2	chr9:108209858-108211101	K562	blood:	n/a	n/a
6	TAF1	chr9:108209924-108210636	ECC-1	luminal epithelium:	n/a	n/a
7	CTCF	chr9:108210180-108210330	AG04450	lung:	n/a	n/a
8	PBX3	chr9:108209940-108210630	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr9:108209861-108210918	GM12878	blood:	n/a	n/a
10	POLR2A	chr9:108210083-108211154	H1-hESC	embryonic stem cell:	n/a	n/a
11	NR2C2	chr9:108210117-108210536	HepG2	liver:	n/a	chr9:108210310-108210325 chr9:108210311-108210324
12	CTCF	chr9:108210160-108210310	GM12867	blood:	n/a	n/a
13	MYC	chr9:108210265-108210418	HepG2	liver:	n/a	n/a
14	YY1	chr9:108209896-108210858	HepG2	liver:	n/a	chr9:108210523-108210534
15	HEY1	chr9:108210000-108210555	HepG2	liver:	n/a	chr9:108210268-108210283 chr9:108210264-108210279 chr9:108210091-108210106
16	POLR2A	chr9:108209943-108210567	HepG2	liver:	n/a	n/a
17	NFIC	chr9:108210056-108210464	GM12878	blood:	n/a	n/a
18	MXI1	chr9:108209566-108212406	SK-N-SH	brain:	n/a	n/a
19	SMC3	chr9:108209821-108210421	GM12878	blood:	n/a	n/a
20	PML	chr9:108209668-108210660	GM12878	blood:	n/a	n/a
21	CTCF	chr9:108210063-108210359	IMR90	lung:	n/a	n/a
22	POLR2A	chr9:108209861-108210685	HUVEC	blood vessel:	n/a	n/a
23	CHD2	chr9:108209938-108210535	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr9:108210160-108210310	NHEK	skin:	n/a	n/a
25	POLR2A	chr9:108210056-108210524	HepG2	liver:	n/a	n/a
26	YY1	chr9:108210008-108210675	K562	blood:	n/a	chr9:108210523-108210534
27	CTCF	chr9:108210078-108210419	MCF-7	breast:	n/a	n/a
28	POLR2A	chr9:108209820-108211094	SK-N-SH	brain:	n/a	n/a
29	MYC	chr9:108209767-108210770	MCF10A-Er-Src	breast:	n/a	chr9:108210570-108210580
30	ZBTB7A	chr9:108209774-108211072	ECC-1	luminal epithelium:	n/a	n/a
31	TAF1	chr9:108209747-108210685	A549	lung:	n/a	n/a
32	CTCF	chr9:108210180-108210330	GM12865	blood:	n/a	n/a
33	TCF3	chr9:108210072-108210513	GM12878	blood:	n/a	n/a
34	POLR2A	chr9:108209899-108211038	GM12878	blood:	n/a	n/a
35	NRF1	chr9:108209979-108210732	SK-N-SH	brain:	n/a	chr9:108210570-108210579 chr9:108210265-108210279 chr9:108210268-108210279 chr9:108210268-108210277 chr9:108210267-108210278 chr9:108210268-108210282
36	CTCF	chr9:108210093-108210332	ProgFib	skin:	n/a	n/a
37	CTCF	chr9:108210160-108210310	A549	lung:	n/a	n/a
38	EP300	chr9:108209990-108210452	H1-hESC	embryonic stem cell:	n/a	chr9:108210094-108210110 chr9:108210271-108210287
39	POLR2A	chr9:108209984-108210742	GM12892	blood:	n/a	n/a
40	CTCF	chr9:108210200-108210350	Caco-2	colon:	n/a	n/a
41	TAF1	chr9:108210168-108210546	K562	blood:	n/a	n/a
42	NR2F2	chr9:108210104-108210483	K562	blood:	n/a	chr9:108210310-108210325
43	CTCF	chr9:108210160-108210310	Hela-S3	cervix:	n/a	n/a
44	E2F6	chr9:108209838-108210535	A549	lung:	n/a	chr9:108210269-108210278
45	TAF1	chr9:108209855-108211165	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAX	chr9:108210131-108210958	K562	blood:	n/a	chr9:108210570-108210580
47	POLR2A	chr9:108209930-108211071	GM18526	blood:	n/a	n/a
48	CTCF	chr9:108210099-108210333	Hela-S3	cervix:	n/a	n/a
49	TAF1	chr9:108209938-108210427	PFSK-1	brain:	n/a	n/a
50	MAX	chr9:108209774-108211166	H1-hESC	embryonic stem cell:	n/a	chr9:108210570-108210580

Variant related genes	Relation type
FSD1L	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10491809	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10816281	1.00[CEU][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10816283	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10816285	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.96[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes]
rs10816286	0.80[EUR][1000 genomes]
rs10816287	0.81[EUR][1000 genomes]
rs10816288	0.81[EUR][1000 genomes]
rs10816289	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes]
rs10820803	0.83[AFR][1000 genomes]
rs10820804	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10820811	0.91[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10820814	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10820815	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10978169	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10978172	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs10978176	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes]
rs10978177	0.89[CEU][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs10978179	0.81[EUR][1000 genomes]
rs10991659	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10991673	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10991677	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10991679	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11562356	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12336250	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12336844	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12337780	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12345599	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12352975	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1327352	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1327355	1.00[CEU][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.96[MKK][hapmap];0.90[YRI][hapmap]
rs1887367	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2296750	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2297023	1.00[ASN][1000 genomes]
rs2417625	0.89[ASW][hapmap];0.91[CEU][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs28542455	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28851907	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3750500	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3793639	0.80[ASW][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes]
rs55798036	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7023302	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7023520	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7033138	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[YRI][hapmap];0.81[EUR][1000 genomes]
rs7033165	0.81[EUR][1000 genomes]
rs7034149	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7037104	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7037141	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7037218	1.00[ASW][hapmap];0.91[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7038407	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7045862	0.80[YRI][hapmap]
rs7047791	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72744263	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72744264	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7852541	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7854411	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7856617	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7857186	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs997319	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108209600-108210400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:108209600-108210400	Active TSS	Brain Germinal Matrix	brain
3	chr9:108209600-108210800	Active TSS	Primary T cells from cord blood	blood
4	chr9:108209600-108211000	Active TSS	Brain Anterior Caudate	brain
5	chr9:108209600-108211000	Active TSS	Rectal Smooth Muscle	rectum
6	chr9:108209600-108211200	Active TSS	Brain Angular Gyrus	brain
7	chr9:108209600-108211400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr9:108209600-108211400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr9:108209600-108211400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr9:108209600-108211400	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr9:108209600-108211400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:108209600-108211400	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr9:108209600-108211400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:108209600-108211400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr9:108209600-108211600	Active TSS	H1 Cell Line	embryonic stem cell
16	chr9:108209600-108211600	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr9:108209600-108211600	Active TSS	Fetal Brain Female	brain
18	chr9:108209600-108211600	Active TSS	Fetal Intestine Small	intestine
19	chr9:108209600-108211600	Active TSS	K562	blood
20	chr9:108209600-108211800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr9:108209600-108211800	Active TSS	Fetal Kidney	kidney
22	chr9:108209600-108211800	Active TSS	NHDF-Ad	bronchial
23	chr9:108209600-108212000	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr9:108209800-108210400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:108209800-108210800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:108209800-108210800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr9:108209800-108210800	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr9:108209800-108210800	Active TSS	Thymus	Thymus
29	chr9:108209800-108210800	Active TSS	Spleen	Spleen
30	chr9:108209800-108211000	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr9:108209800-108211000	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr9:108209800-108211000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr9:108209800-108211000	Active TSS	Fetal Lung	lung
34	chr9:108209800-108211000	Active TSS	Small Intestine	intestine
35	chr9:108209800-108211200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr9:108209800-108211200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:108209800-108211200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr9:108209800-108211200	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr9:108209800-108211200	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr9:108209800-108211200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:108209800-108211200	Active TSS	Aorta	Aorta
42	chr9:108209800-108211200	Active TSS	Lung	lung
43	chr9:108209800-108211200	Active TSS	Ovary	ovary
44	chr9:108209800-108211400	Active TSS	Colon Smooth Muscle	Colon
45	chr9:108209800-108211400	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr9:108209800-108212000	Active TSS	HSMMtube	muscle
47	chr9:108209800-108212200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:108209800-108212400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:108209800-108212800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr9:108210000-108210400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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