Variant report

Variant	rs61109654
Chromosome Location	chr3:112218767-112218768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr3:112214327-112218844	GM12878	blood:	n/a	n/a
2	NFIC	chr3:112216704-112218950	GM12878	blood:	n/a	n/a
3	CEBPB	chr3:112216960-112218902	GM12878	blood:	n/a	n/a
4	RUNX3	chr3:112217342-112218941	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:112214030-112219273	GM12891	blood:	n/a	n/a
6	POLR2A	chr3:112217436-112218779	GM12892	blood:	n/a	n/a
7	MTA3	chr3:112215960-112218798	GM12878	blood:	n/a	n/a
8	NFIC	chr3:112216802-112218904	GM12878	blood:	n/a	n/a
9	TBP	chr3:112217563-112218817	GM12878	blood:	n/a	n/a
10	SPI1	chr3:112218725-112218930	GM12891	blood:	n/a	chr3:112218838-112218851 chr3:112218851-112218864
11	FOXM1	chr3:112217762-112218785	GM12878	blood:	n/a	n/a
12	MXI1	chr3:112217406-112218902	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:112218761-112218811	PANC-1	pancreas:	n/a
2	chr3:112218761-112218811	HMEC	breast:	n/a
3	chr3:112218761-112218811	GM06990	blood:	n/a
4	chr3:112218761-112218811	K562	blood:	n/a
5	chr3:112218761-112218811	AG04450	lung:	fetal
6	chr3:112218761-112218811	Hela-S3	cervix:	n/a
7	chr3:112218761-112218811	MCF10A-Er-Src	breast:	n/a
8	chr3:112218761-112218811	HCF	heart:	n/a
9	chr3:112218761-112218811	HCM	heart:	n/a
10	chr3:112218761-112218811	NHBE	bronchial:	n/a
11	chr3:112218761-112218811	GM19239	blood:	n/a
12	chr3:112218761-112218811	BE2_C	brain:	n/a
13	chr3:112218761-112218811	Caco-2	colon:	n/a
14	chr3:112218761-112218811	A549	lung:	n/a
15	chr3:112218761-112218811	SK-N-SH_RA	brain:	n/a
16	chr3:112218761-112218811	Hepatocyte	liver:	n/a
17	chr3:112218761-112218811	U87	brain:	n/a
18	chr3:112218761-112218811	RPTEC	kidney:	n/a
19	chr3:112218761-112218811	HIPEpiC	eye:	n/a
20	chr3:112218761-112218811	AG10803	skin:	n/a
21	chr3:112218761-112218811	ovcar-3	ovarian:	n/a
22	chr3:112218761-112218811	HCPEpiC	choroid plexus:	n/a
23	chr3:112218761-112218811	PFSK-1	brain:	n/a
24	chr3:112218761-112218811	ECC-1	luminal epithelium:	n/a
25	chr3:112218761-112218811	GM12878	blood:	n/a
26	chr3:112218761-112218811	HEEpiC	esophagus:	n/a
27	chr3:112218761-112218811	NB4	blood:	n/a
28	chr3:112218761-112218811	SK-N-MC	brain:	n/a
29	chr3:112218761-112218811	IMR90	lung:	fetal
30	chr3:112218761-112218811	GM12891	blood:	n/a
31	chr3:112218761-112218811	AG09309	skin:	n/a
32	chr3:112218761-112218811	SKMC	muscle:	n/a
33	chr3:112218761-112218811	AG04449	skin:	fetal
34	chr3:112218761-112218811	HRPEpiC	eye:	n/a
35	chr3:112218761-112218811	PrEC	prostate:	n/a
36	chr3:112218761-112218811	MCF-7	breast:	n/a
37	chr3:112218761-112218811	HNPCEpiC	eye:	n/a
38	chr3:112218761-112218811	BJ	skin:	n/a
39	chr3:112218761-112218811	NH-A	brain:	n/a
40	chr3:112218761-112218811	HAEpiC	amniotic membrane:	n/a
41	chr3:112218761-112218811	GM12892	blood:	n/a
42	chr3:112218761-112218811	AG09319	gingival:	n/a
43	chr3:112218761-112218811	ProgFib	skin:	n/a
44	chr3:112218761-112218811	SAEC	small airway:	n/a
45	chr3:112218761-112218811	Jurkat	blood:	n/a
46	chr3:112218761-112218811	HEK293	kidney:	embryo
47	chr3:112218761-112218811	HRCEpiC	kidney:	n/a
48	chr3:112218761-112218811	H1-hESC	embryonic stem cell:	embryo
49	chr3:112218761-112218811	NHDF-neo	bronchial:	n/a
50	chr3:112218761-112218811	HRE	kidney:	n/a

No data

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

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs16859674	0.94[AFR][1000 genomes]
rs1817694	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1906519	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56231377	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57024033	1.00[EUR][1000 genomes]
rs57496061	1.00[EUR][1000 genomes]
rs57606986	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58720291	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60286828	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60526457	1.00[EUR][1000 genomes]
rs60780375	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6438081	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6792289	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72938427	1.00[EUR][1000 genomes]
rs73853430	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73853433	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73853435	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73853437	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7612986	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010208	chr3:112098542-112227212	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112214600-112228600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:112215800-112218800	Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr3:112216200-112218800	Active TSS	Primary T killer memory cells from peripheral blood	blood
4	chr3:112216600-112219200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr3:112218000-112218800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:112218000-112219000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:112218200-112218800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr3:112218200-112218800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:112218200-112218800	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr3:112218200-112219000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr3:112218400-112218800	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr3:112218400-112219000	Enhancers	Primary hematopoietic stem cells	blood
13	chr3:112218400-112219200	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr3:112218400-112220000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:112218400-112220600	Enhancers	HUVEC	blood vessel
16	chr3:112218600-112218800	Active TSS	Primary T cells from cord blood	blood
17	chr3:112218600-112218800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:112218600-112218800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr3:112218600-112219000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr3:112218600-112219000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr3:112218600-112219200	Flanking Active TSS	GM12878-XiMat	blood
22	chr3:112218600-112222400	Weak transcription	Fetal Thymus	thymus

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