Variant report

Variant	rs6666314
Chromosome Location	chr1:246671213-246671214
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	HCFC1	chr1:246669709-246671402	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:246670111-246671325	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:246670206-246671264	K562	blood:	n/a	n/a
4	E2F6	chr1:246670293-246671410	H1-hESC	embryonic stem cell:	n/a	chr1:246670594-246670603 chr1:246670635-246670644
5	CBX3	chr1:246670288-246671321	K562	blood:	n/a	n/a
6	POLR2A	chr1:246670259-246671245	HepG2	liver:	n/a	n/a
7	MAX	chr1:246669528-246671262	K562	blood:	n/a	chr1:246669960-246669969 chr1:246670291-246670301 chr1:246670742-246670751 chr1:246669971-246669980
8	MXI1	chr1:246669353-246671469	SK-N-SH	brain:	n/a	chr1:246670736-246670751

Variant related genes	Relation type
SMYD3	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10158851	0.90[ASN][1000 genomes]
rs10218761	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10754519	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10802414	0.90[ASN][1000 genomes]
rs10802415	0.90[ASN][1000 genomes]
rs10802416	0.88[ASN][1000 genomes]
rs10802423	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10924752	0.90[ASN][1000 genomes]
rs10924753	0.90[ASN][1000 genomes]
rs10924754	0.90[ASN][1000 genomes]
rs1890158	0.82[ASN][1000 genomes]
rs2152887	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2340782	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4040219	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4081311	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4654276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4654279	0.85[ASN][1000 genomes]
rs6660942	0.90[ASN][1000 genomes]
rs6673969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520453	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7531320	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004119	chr1:245957145-246813150	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv535389	chr1:245957145-246813150	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1014529	chr1:245957145-246817877	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1000654	chr1:245966390-246778182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv535392	chr1:245966390-246778182	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv868852	chr1:245969229-246811220	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv948348	chr1:246090818-246853200	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv430402	chr1:246124959-246787448	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv497890	chr1:246143172-246778453	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv998930	chr1:246166737-246702012	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1005825	chr1:246174208-246688635	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv535398	chr1:246194546-246686301	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv1001462	chr1:246194546-246686358	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv535399	chr1:246194546-246686358	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv949329	chr1:246220147-246710091	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv468839	chr1:246303128-246708467	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv549528	chr1:246303128-246708467	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv1005573	chr1:246378676-246740427	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats 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	16 gene(s)	inside rSNPs	diseases
19	nsv535405	chr1:246378676-246740427	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
20	nsv549531	chr1:246406762-246681116	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
21	esv2757779	chr1:246407146-246740944	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	esv2759012	chr1:246407146-246740944	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
23	nsv428346	chr1:246407146-246740944	Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
24	nsv1013800	chr1:246472691-246840960	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
25	nsv535409	chr1:246472691-246840960	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
26	nsv997661	chr1:246482924-246702012	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
27	esv2762191	chr1:246546436-246815064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
28	nsv1006777	chr1:246585396-246702012	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
29	nsv535412	chr1:246585396-246702012	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
30	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
31	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
32	nsv1010453	chr1:246645797-246815052	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
33	nsv998579	chr1:246666041-246817877	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
34	esv1822854	chr1:246668544-246685307	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
35	nsv522303	chr1:246668544-246692992	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
36	nsv525447	chr1:246668544-246698653	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246669400-246671400	Active TSS	Rectal Smooth Muscle	rectum
2	chr1:246669800-246671400	Active TSS	Colonic Mucosa	Colon
3	chr1:246670000-246671400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:246670000-246671400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:246670000-246671400	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr1:246670600-246671400	Flanking Active TSS	Dnd41	blood
7	chr1:246670800-246671400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr1:246670800-246671400	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr1:246670800-246671400	Enhancers	Spleen	Spleen
10	chr1:246670800-246671400	Flanking Active TSS	Hela-S3	cervix
11	chr1:246671000-246671400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:246671000-246671400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr1:246671000-246671400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:246671000-246671400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr1:246671000-246671400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr1:246671000-246672200	Enhancers	HepG2	liver
17	chr1:246671200-246671400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:246671200-246671400	Enhancers	Primary B cells from peripheral blood	blood
19	chr1:246671200-246671400	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr1:246671200-246671400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr1:246671200-246671400	Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr1:246671200-246671400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:246671200-246671400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:246671200-246671400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:246671200-246671400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:246671200-246671400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr1:246671200-246671400	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr1:246671200-246671400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:246671200-246671400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:246671200-246671400	Enhancers	Colon Smooth Muscle	Colon
31	chr1:246671200-246671400	Enhancers	Fetal Thymus	thymus
32	chr1:246671200-246671400	Active TSS	Stomach Smooth Muscle	stomach
33	chr1:246671200-246671400	Enhancers	Thymus	Thymus
34	chr1:246671200-246671400	Enhancers	K562	blood
35	chr1:246671200-246671400	Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:246671200-246671800	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr1:246671200-246672200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:246671200-246675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:246671200-246676000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links