Variant report

Variant	rs11165878
Chromosome Location	chr1:92415049-92415050
allele	C/G
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	NFYB	chr1:92414606-92415093	K562	blood:	n/a	n/a
2	USF1	chr1:92414687-92415082	H1-hESC	embryonic stem cell:	n/a	chr1:92414872-92414893 chr1:92414877-92414886 chr1:92414878-92414887 chr1:92414878-92414887 chr1:92414879-92414888 chr1:92414876-92414889
3	USF1	chr1:92414762-92415061	H1-hESC	embryonic stem cell:	n/a	chr1:92414872-92414893 chr1:92414877-92414886 chr1:92414878-92414887 chr1:92414878-92414887 chr1:92414879-92414888 chr1:92414876-92414889
4	USF1	chr1:92414702-92415089	K562	blood:	n/a	chr1:92414872-92414893 chr1:92414877-92414886 chr1:92414878-92414887 chr1:92414878-92414887 chr1:92414879-92414888 chr1:92414876-92414889
5	USF2	chr1:92414773-92415057	HepG2	liver:	n/a	chr1:92414872-92414893 chr1:92414877-92414886 chr1:92414878-92414887 chr1:92414878-92414887 chr1:92414879-92414888 chr1:92414876-92414889

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:92415048-92415098	MCF-7	breast:	n/a
2	chr1:92415048-92415098	SK-N-SH	brain:	n/a
3	chr1:92415048-92415098	HepG2	liver:	n/a
4	chr1:92415048-92415098	HRPEpiC	eye:	n/a
5	chr1:92415048-92415098	HEK293	kidney:	embryo
6	chr1:92415048-92415098	HRE	kidney:	n/a
7	chr1:92415048-92415098	PFSK-1	brain:	n/a
8	chr1:92415048-92415098	AoSMC	blood vessel:	n/a
9	chr1:92415048-92415098	BJ	skin:	n/a
10	chr1:92415048-92415098	RPTEC	kidney:	n/a
11	chr1:92415048-92415098	Caco-2	colon:	n/a
12	chr1:92415048-92415098	HAEpiC	amniotic membrane:	n/a
13	chr1:92415048-92415098	GM12892	blood:	n/a
14	chr1:92415048-92415098	AG04449	skin:	fetal
15	chr1:92415048-92415098	HCM	heart:	n/a
16	chr1:92415048-92415098	A549	lung:	n/a
17	chr1:92415048-92415098	U87	brain:	n/a
18	chr1:92415048-92415098	H1-hESC	embryonic stem cell:	embryo
19	chr1:92415048-92415098	ECC-1	luminal epithelium:	n/a
20	chr1:92415048-92415098	PANC-1	pancreas:	n/a
21	chr1:92415048-92415098	Hela-S3	cervix:	n/a
22	chr1:92415048-92415098	IMR90	lung:	fetal
23	chr1:92415048-92415098	SK-N-SH_RA	brain:	n/a
24	chr1:92415048-92415098	HL-60	blood:	n/a
25	chr1:92415048-92415098	HRCEpiC	kidney:	n/a
26	chr1:92415048-92415098	HMEC	breast:	n/a
27	chr1:92415048-92415098	NHBE	bronchial:	n/a
28	chr1:92415048-92415098	HUVEC	blood vessel:	n/a
29	chr1:92415048-92415098	Hepatocyte	liver:	n/a
30	chr1:92415048-92415098	HIPEpiC	eye:	n/a
31	chr1:92415048-92415098	HCPEpiC	choroid plexus:	n/a
32	chr1:92415048-92415098	BE2_C	brain:	n/a
33	chr1:92415048-92415098	GM12878	blood:	n/a
34	chr1:92415048-92415098	AG09309	skin:	n/a
35	chr1:92415048-92415098	GM06990	blood:	n/a
36	chr1:92415048-92415098	NHDF-neo	bronchial:	n/a
37	chr1:92415048-92415098	Jurkat	blood:	n/a
38	chr1:92415048-92415098	SAEC	small airway:	n/a
39	chr1:92415048-92415098	NH-A	brain:	n/a
40	chr1:92415048-92415098	ProgFib	skin:	n/a
41	chr1:92415048-92415098	NB4	blood:	n/a
42	chr1:92415048-92415098	HPAEpiC	pulmonary alveolar:	n/a
43	chr1:92415048-92415098	HEEpiC	esophagus:	n/a
44	chr1:92415048-92415098	GM19239	blood:	n/a
45	chr1:92415048-92415098	CMK	blood:	n/a
46	chr1:92415048-92415098	HCT-116	colon:	n/a
47	chr1:92415048-92415098	K562	blood:	n/a
48	chr1:92415048-92415098	SK-N-MC	brain:	n/a
49	chr1:92415048-92415098	MCF10A-Er-Src	breast:	n/a
50	chr1:92415048-92415098	HCF	heart:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPHX4-2	chr1:92414955-92415076	NONHSAT004444
2	lnc-EPHX4-2	chr1:92414960-92415076	NONHSAT004446

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

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1073001	0.83[CHB][hapmap]
rs10783071	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs10783072	0.83[CHB][hapmap];0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs10783074	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.96[TSI][hapmap]
rs10875067	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875068	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875081	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875082	0.90[ASN][1000 genomes]
rs10875083	0.80[ASN][1000 genomes]
rs10875096	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10875101	0.85[ASN][1000 genomes]
rs11165840	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[ASN][1000 genomes]
rs11165842	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap]
rs11165853	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11165885	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165898	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165904	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12040031	0.97[ASN][1000 genomes]
rs12060343	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12725353	0.86[ASN][1000 genomes]
rs12732002	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12733726	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12741192	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1328593	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs1887812	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767854	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3767855	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4658118	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4658119	0.97[ASN][1000 genomes]
rs4658123	0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4658281	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4658283	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4658286	0.86[CHB][hapmap];0.80[CHD][hapmap];0.84[ASN][1000 genomes]
rs61779126	0.90[ASN][1000 genomes]
rs6656817	0.94[ASN][1000 genomes]
rs6666624	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6677351	0.97[ASN][1000 genomes]
rs6686166	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6689033	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6690705	0.91[GIH][hapmap]
rs6692045	0.91[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap]
rs6696267	0.83[CHB][hapmap]
rs6697441	0.91[GIH][hapmap]
rs6702511	0.94[ASN][1000 genomes]
rs7541712	0.97[ASN][1000 genomes]
rs7551956	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs7553278	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs766665	0.97[ASN][1000 genomes]
rs766666	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs928015	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9803619	0.94[ASN][1000 genomes]
rs9887935	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv546819	chr1:92256626-92558583	Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv546820	chr1:92273644-92558583	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv530046	chr1:92277460-92799794	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
21	nsv1007270	chr1:92289298-92598800	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv1002730	chr1:92302541-92565229	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv830581	chr1:92317207-92511175	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
24	nsv871415	chr1:92340684-92641607	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
25	esv2750842	chr1:92356781-92579675	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
26	nsv871144	chr1:92380302-92641607	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92413000-92415400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr1:92414400-92415400	Flanking Active TSS	Placenta	Placenta
3	chr1:92414600-92415600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:92414800-92415400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr1:92414800-92415400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:92414800-92415600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr1:92415000-92415400	Enhancers	Primary T cells fromperipheralblood	blood
8	chr1:92415000-92427800	Weak transcription	Right Atrium	heart

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