Variant report

Variant	rs706617
Chromosome Location	chr13:50703185-50703186
allele	A/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	RUNX3	chr13:50702687-50703711	GM12878	blood:	n/a	n/a
2	NFIC	chr13:50702699-50703647	GM12878	blood:	n/a	n/a
3	POLR2A	chr13:50697801-50703833	H1-neurons	neurons:	n/a	n/a
4	FOXM1	chr13:50702773-50703532	GM12878	blood:	n/a	n/a
5	EP300	chr13:50702899-50703569	GM12878	blood:	n/a	chr13:50703109-50703118 chr13:50703105-50703119
6	ATF2	chr13:50703040-50703571	GM12878	blood:	n/a	n/a
7	RUNX3	chr13:50702692-50703595	GM12878	blood:	n/a	n/a
8	MTA3	chr13:50702658-50704187	GM12878	blood:	n/a	n/a
9	ATF2	chr13:50702667-50703620	GM12878	blood:	n/a	n/a
10	BCLAF1	chr13:50703159-50703582	GM12878	blood:	n/a	chr13:50703214-50703223
11	MEF2A	chr13:50703132-50703493	GM12878	blood:	n/a	chr13:50703155-50703170 chr13:50703155-50703172
12	IRF4	chr13:50702849-50703584	GM12878	blood:	n/a	n/a
13	SP1	chr13:50703147-50703612	H1-hESC	embryonic stem cell:	n/a	n/a
14	BCLAF1	chr13:50702758-50703589	GM12878	blood:	n/a	chr13:50703214-50703223
15	EBF1	chr13:50702929-50703919	GM12878	blood:	n/a	chr13:50703698-50703708 chr13:50703697-50703708 chr13:50703697-50703710 chr13:50703699-50703708
16	NFATC1	chr13:50703162-50703599	GM12878	blood:	n/a	n/a
17	RELA	chr13:50702760-50703569	GM19193	blood:	n/a	n/a
18	TBL1XR1	chr13:50702829-50703583	GM12878	blood:	n/a	n/a
19	BHLHE40	chr13:50702892-50703574	GM12878	blood:	n/a	n/a
20	NFIC	chr13:50702752-50703695	GM12878	blood:	n/a	n/a
21	RELA	chr13:50702743-50703645	GM19099	blood:	n/a	n/a
22	ZNF384	chr13:50703166-50703617	GM12878	blood:	n/a	n/a
23	FOXM1	chr13:50702626-50703713	GM12878	blood:	n/a	n/a
24	STAT5A	chr13:50702577-50703636	GM12878	blood:	n/a	n/a
25	POLR2A	chr13:50697768-50704046	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:50702418..50705052-chr13:50749467..50751961,2	K562	blood:
2	chr13:50661950..50663880-chr13:50702187..50703696,2	MCF-7	breast:
3	chr13:50652169..50667024-chr13:50693268..50703943,57	K562	blood:
4	chr13:50702118..50703932-chr13:50761814..50763532,2	K562	blood:
5	chr13:50701973..50704283-chr13:50721601..50723228,2	MCF-7	breast:
6	chr13:50654107..50658671-chr13:50702301..50706921,6	MCF-7	breast:
7	chr13:50653006..50665770-chr13:50696335..50703879,43	K562	blood:

Variant related genes	Relation type
DLEU2	TF binding region
ENSG00000231607	Chromatin interaction
ENSG00000176124	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2066550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2472395	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2476389	0.82[EUR][1000 genomes]
rs2476391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2490636	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2490637	0.82[EUR][1000 genomes]
rs2490638	0.82[EUR][1000 genomes]
rs2490639	0.82[EUR][1000 genomes]
rs2687933	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2687934	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2687935	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2687936	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812223	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34047395	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs706609	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73489867	0.82[EUR][1000 genomes]
rs790528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790529	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790531	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs790928	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790931	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs790934	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs790935	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790940	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs790941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832608	chr13:50678628-50888413	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1041501	chr13:50683189-50795195	Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50700600-50703200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
2	chr13:50700600-50703800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
3	chr13:50700800-50703600	Weak transcription	HSMMtube	muscle
4	chr13:50701000-50703800	Weak transcription	HSMM	muscle
5	chr13:50701200-50703400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
6	chr13:50701200-50703600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr13:50701200-50704200	Weak transcription	A549	lung
8	chr13:50701400-50703800	Weak transcription	Hela-S3	cervix
9	chr13:50701600-50705800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
10	chr13:50701800-50703600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:50701800-50704000	Weak transcription	Gastric	stomach
12	chr13:50702000-50703400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr13:50702000-50703400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr13:50702000-50703400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr13:50702000-50703400	Weak transcription	NHLF	lung
16	chr13:50702000-50703400	Weak transcription	Osteobl	bone
17	chr13:50702000-50703600	Weak transcription	Psoas Muscle	Psoas
18	chr13:50702000-50703600	Weak transcription	Right Ventricle	heart
19	chr13:50702000-50703800	Bivalent Enhancer	Fetal Lung	lung
20	chr13:50702200-50703400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr13:50702200-50703400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr13:50702200-50703400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr13:50702200-50703600	Enhancers	Primary B cells from cord blood	blood
24	chr13:50702200-50703600	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr13:50702200-50703800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
26	chr13:50702200-50704000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
27	chr13:50702400-50703400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr13:50702400-50703600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
29	chr13:50702400-50703600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr13:50702400-50703600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr13:50702400-50703600	Weak transcription	Right Atrium	heart
32	chr13:50702400-50703800	Weak transcription	Left Ventricle	heart
33	chr13:50702400-50704000	Bivalent Enhancer	Fetal Intestine Large	intestine
34	chr13:50702400-50704000	Bivalent Enhancer	Fetal Intestine Small	intestine
35	chr13:50702600-50703200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
36	chr13:50702600-50703200	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
37	chr13:50702600-50703400	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr13:50702600-50704200	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
39	chr13:50702600-50704400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
40	chr13:50702800-50703200	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr13:50702800-50703400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
42	chr13:50702800-50703400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:50702800-50703400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr13:50702800-50703400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
45	chr13:50702800-50703600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
46	chr13:50702800-50703600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
47	chr13:50702800-50704600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
48	chr13:50703000-50703200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
49	chr13:50703000-50703200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
50	chr13:50703000-50703200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links