Variant report

Variant	rs9754
Chromosome Location	chr17:34261831-34261832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:122)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:34261789-34261839	HRPEpiC	eye:	n/a
2	chr17:34261789-34261839	SK-N-SH_RA	brain:	n/a
3	chr17:34261789-34261839	AG09309	skin:	n/a
4	chr17:34261789-34261839	LNCaP	prostate:	n/a
5	chr17:34261810-34261860	A549	lung:	n/a
6	chr17:34261810-34261860	HCM	heart:	n/a
7	chr17:34261810-34261860	GM19239	blood:	n/a
8	chr17:34261810-34261860	HL-60	blood:	n/a
9	chr17:34261789-34261839	HCM	heart:	n/a
10	chr17:34261810-34261860	K562	blood:	n/a
11	chr17:34261810-34261860	MCF-7	breast:	n/a
12	chr17:34261789-34261839	AoSMC	blood vessel:	n/a
13	chr17:34261789-34261839	MCF10A-Er-Src	breast:	n/a
14	chr17:34261789-34261839	SK-N-MC	brain:	n/a
15	chr17:34261810-34261860	U87	brain:	n/a
16	chr17:34261810-34261860	MCF10A-Er-Src	breast:	n/a
17	chr17:34261810-34261860	HCPEpiC	choroid plexus:	n/a
18	chr17:34261810-34261860	SK-N-SH_RA	brain:	n/a
19	chr17:34261810-34261860	HMEC	breast:	n/a
20	chr17:34261789-34261839	HEK293	kidney:	embryo
21	chr17:34261789-34261839	NHBE	bronchial:	n/a
22	chr17:34261789-34261839	ECC-1	luminal epithelium:	n/a
23	chr17:34261810-34261860	NT2-D1	testis:	n/a
24	chr17:34261810-34261860	ProgFib	skin:	n/a
25	chr17:34261810-34261860	SAEC	small airway:	n/a
26	chr17:34261810-34261860	Hela-S3	cervix:	n/a
27	chr17:34261789-34261839	HMEC	breast:	n/a
28	chr17:34261789-34261839	Hela-S3	cervix:	n/a
29	chr17:34261789-34261839	BJ	skin:	n/a
30	chr17:34261789-34261839	CMK	blood:	n/a
31	chr17:34261810-34261860	GM06990	blood:	n/a
32	chr17:34261789-34261839	T-47D	breast:	n/a
33	chr17:34261789-34261839	SAEC	small airway:	n/a
34	chr17:34261810-34261860	ECC-1	luminal epithelium:	n/a
35	chr17:34261789-34261839	HepG2	liver:	n/a
36	chr17:34261789-34261839	MCF-7	breast:	n/a
37	chr17:34261789-34261839	HPAEpiC	pulmonary alveolar:	n/a
38	chr17:34261789-34261839	PFSK-1	brain:	n/a
39	chr17:34261810-34261860	IMR90	lung:	fetal
40	chr17:34261789-34261839	SK-N-SH	brain:	n/a
41	chr17:34261789-34261839	PrEC	prostate:	n/a
42	chr17:34261810-34261860	HEEpiC	esophagus:	n/a
43	chr17:34261789-34261839	ProgFib	skin:	n/a
44	chr17:34261810-34261860	PrEC	prostate:	n/a
45	chr17:34261789-34261839	NB4	blood:	n/a
46	chr17:34261810-34261860	HRE	kidney:	n/a
47	chr17:34261789-34261839	HCPEpiC	choroid plexus:	n/a
48	chr17:34261810-34261860	BJ	skin:	n/a
49	chr17:34261789-34261839	NHDF-neo	bronchial:	n/a
50	chr17:34261810-34261860	NB4	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:34257735..34259695-chr17:34260780..34264924,4	K562	blood:

No data

Variant related genes	Relation type
RDM1	CpG island
ENSG00000187456	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs11080360	0.86[ASN][1000 genomes]
rs11080361	0.86[ASN][1000 genomes]
rs11080362	0.86[ASN][1000 genomes]
rs11650409	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11652536	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs11653016	0.86[ASN][1000 genomes]
rs11653051	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11653204	0.85[ASN][1000 genomes]
rs11654713	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11655533	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11656556	0.85[ASN][1000 genomes]
rs11657908	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11868801	0.86[ASN][1000 genomes]
rs11869976	0.86[ASN][1000 genomes]
rs16971670	0.86[ASN][1000 genomes]
rs2107538	0.92[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2107540	0.85[ASN][1000 genomes]
rs2251660	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280787	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291299	0.96[TSI][hapmap]
rs2376287	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2526327	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2526328	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2702947	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2702948	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2735475	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28550999	0.86[ASN][1000 genomes]
rs28722787	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28739295	0.85[ASN][1000 genomes]
rs28912068	0.82[ASN][1000 genomes]
rs34369685	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3760447	0.82[ASN][1000 genomes]
rs3809769	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs3817655	0.82[EUR][1000 genomes]
rs3826404	0.89[TSI][hapmap]
rs4251751	0.94[JPT][hapmap]
rs4251752	0.94[JPT][hapmap]
rs4795089	0.87[JPT][hapmap]
rs4795090	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs4795095	0.94[JPT][hapmap]
rs4795099	0.81[ASN][1000 genomes]
rs4795100	0.86[ASN][1000 genomes]
rs4795101	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4796105	0.88[TSI][hapmap]
rs4796107	0.87[JPT][hapmap]
rs4796108	0.88[JPT][hapmap]
rs4796112	0.94[JPT][hapmap]
rs4796114	0.85[JPT][hapmap]
rs4796115	0.94[JPT][hapmap]
rs4796118	0.94[JPT][hapmap]
rs4796119	0.93[JPT][hapmap]
rs4796120	0.94[JPT][hapmap]
rs4796123	0.80[ASN][1000 genomes]
rs4796124	0.85[ASN][1000 genomes]
rs4796125	0.85[ASN][1000 genomes]
rs4796126	0.83[ASN][1000 genomes]
rs4796127	0.85[ASN][1000 genomes]
rs4796128	0.95[GIH][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs4796130	0.86[ASN][1000 genomes]
rs4796131	0.86[ASN][1000 genomes]
rs4796133	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4796134	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4796136	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4796137	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4796138	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56294660	0.86[ASN][1000 genomes]
rs56344830	0.83[ASN][1000 genomes]
rs59338510	0.85[ASN][1000 genomes]
rs6505496	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs7211393	0.85[EUR][1000 genomes]
rs7213636	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7215845	0.87[EUR][1000 genomes]
rs8066406	0.88[EUR][1000 genomes]
rs9303691	0.94[JPT][hapmap]
rs9303693	0.86[ASN][1000 genomes]
rs9789051	0.85[ASN][1000 genomes]
rs9889274	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs9889977	0.86[ASN][1000 genomes]
rs9890583	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9891064	0.86[ASN][1000 genomes]
rs9893004	0.86[ASN][1000 genomes]
rs9894314	0.86[ASN][1000 genomes]
rs9894799	0.86[ASN][1000 genomes]
rs9896265	0.85[ASN][1000 genomes]
rs9896658	0.86[ASN][1000 genomes]
rs9897665	0.86[ASN][1000 genomes]
rs9898132	0.94[JPT][hapmap]
rs9898152	0.94[JPT][hapmap]
rs9899215	0.86[ASN][1000 genomes]
rs9899866	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9899870	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9899881	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9900236	0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9901195	0.86[ASN][1000 genomes]
rs9901418	0.86[ASN][1000 genomes]
rs9903590	0.86[ASN][1000 genomes]
rs9904675	0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9907145	0.86[ASN][1000 genomes]
rs9907295	0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9908011	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9908525	0.86[ASN][1000 genomes]
rs9909050	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9911016	0.86[ASN][1000 genomes]
rs9912049	0.86[ASN][1000 genomes]
rs9912284	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9912571	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9912793	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9912894	0.86[ASN][1000 genomes]
rs9913488	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9913559	0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9914401	0.94[JPT][hapmap]
rs9914468	0.86[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	esv3380735	chr17:34246253-34271932	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1063100	chr17:34246253-34397598	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv833424	chr17:34246253-34419476	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1056950	chr17:34246253-34442620	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1059795	chr17:34246253-34442620	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1060457	chr17:34246253-34442620	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv543320	chr17:34246253-34442620	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv949160	chr17:34246253-34442620	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9754	AMAC1	cis	cerebellum	SCAN
rs9754	C17orf50	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34257800-34264000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:34257800-34266200	Weak transcription	Aorta	Aorta
3	chr17:34258000-34273800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:34258400-34263400	Weak transcription	Fetal Intestine Large	intestine
5	chr17:34259400-34263600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:34259800-34263400	Weak transcription	Fetal Intestine Small	intestine
7	chr17:34260000-34264600	Weak transcription	K562	blood
8	chr17:34261600-34262600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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