Variant report

Variant	rs17132744
Chromosome Location	chr7:2874982-2874983
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	GATA3	chr7:2874530-2875202	MCF-7	breast:	n/a	chr7:2874952-2874962
2	CEBPB	chr7:2874491-2875044	H1-hESC	embryonic stem cell:	n/a	chr7:2874902-2874913 chr7:2874900-2874911
3	ZNF217	chr7:2874521-2874991	MCF-7	breast:	n/a	n/a
4	FOS	chr7:2874371-2875043	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr7:2874421-2875067	HepG2	liver:	n/a	chr7:2874902-2874913 chr7:2874900-2874911
6	MYC	chr7:2874313-2875032	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr7:2874403-2875054	IMR90	lung:	n/a	chr7:2874902-2874913 chr7:2874900-2874911
8	CEBPB	chr7:2874505-2875046	A549	lung:	n/a	chr7:2874902-2874913 chr7:2874900-2874911
9	SIN3AK20	chr7:2874224-2875358	MCF-7	breast:	n/a	n/a
10	CEBPB	chr7:2874432-2875005	K562	blood:	n/a	chr7:2874902-2874913 chr7:2874900-2874911
11	CEBPB	chr7:2874492-2875053	Hela-S3	cervix:	n/a	chr7:2874902-2874913 chr7:2874900-2874911
12	CEBPB	chr7:2874310-2875160	MCF-7	breast:	n/a	chr7:2874902-2874913 chr7:2874900-2874911
13	GATA3	chr7:2874559-2875213	MCF-7	breast:	n/a	chr7:2874952-2874962
14	STAT3	chr7:2874382-2875011	MCF10A-Er-Src	breast:	n/a	chr7:2874902-2874910
15	CEBPB	chr7:2874463-2875084	MCF-7	breast:	n/a	chr7:2874902-2874913 chr7:2874900-2874911
16	FOS	chr7:2874386-2875032	MCF10A-Er-Src	breast:	n/a	n/a
17	GATA3	chr7:2874703-2875107	T-47D	breast:	n/a	chr7:2874952-2874962
18	GATA3	chr7:2874701-2875123	T-47D	breast:	n/a	chr7:2874952-2874962

No.	Distal block	Cell Line	Cell type
1	chr7:2873423..2874992-chr7:2887430..2888992,2	MCF-7	breast:
2	chr7:2872743..2875246-chr7:2912589..2914983,2	MCF-7	breast:
3	chr7:2869377..2877481-chr7:2880306..2885399,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231357	TF binding region
ENSG00000146535	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11761804	0.91[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs11765386	0.93[MEX][hapmap];0.81[AMR][1000 genomes]
rs11765473	0.81[AMR][1000 genomes]
rs11765492	0.89[CEU][hapmap]
rs11765726	0.84[CEU][hapmap];0.89[AMR][1000 genomes]
rs11766514	0.81[AMR][1000 genomes]
rs11768001	0.84[AMR][1000 genomes]
rs11769532	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11769669	0.81[AMR][1000 genomes]
rs11770710	0.81[AMR][1000 genomes]
rs11772176	0.84[AMR][1000 genomes]
rs11772508	0.87[GIH][hapmap];0.93[MEX][hapmap]
rs11971014	0.89[CEU][hapmap]
rs12540539	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17132624	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs17132741	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17241904	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17300022	0.91[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs28706013	0.82[AMR][1000 genomes]
rs35450876	0.81[AMR][1000 genomes]
rs55832916	0.81[AMR][1000 genomes]
rs56007918	0.91[AMR][1000 genomes]
rs56296737	0.84[AMR][1000 genomes]
rs6945135	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6964740	0.86[AMR][1000 genomes]
rs6967664	0.88[AMR][1000 genomes]
rs73033403	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73033407	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73033408	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73033412	0.84[AMR][1000 genomes]
rs73033417	0.81[AMR][1000 genomes]
rs73033432	0.82[AMR][1000 genomes]
rs73033457	0.80[AMR][1000 genomes]
rs73049305	0.81[AMR][1000 genomes]
rs73049331	0.81[AMR][1000 genomes]
rs73049362	0.91[AMR][1000 genomes]
rs73049380	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73051415	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73051444	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73051469	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs757788	0.91[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7803944	0.81[AMR][1000 genomes]
rs7804264	0.84[AMR][1000 genomes]
rs7811164	0.86[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	nsv1029250	chr7:2722737-2881021	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv538652	chr7:2722737-2881021	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1015700	chr7:2753965-2945848	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1022612	chr7:2789555-3019200	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1018162	chr7:2817460-2891181	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv538655	chr7:2817460-2891181	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv1019463	chr7:2848448-2881872	Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17132744	PRKAR1B	cis	parietal	SCAN
rs17132744	C7orf50	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:2851800-2882800	Weak transcription	Aorta	Aorta
2	chr7:2861000-2881800	Weak transcription	Colonic Mucosa	Colon
3	chr7:2861200-2877000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr7:2861400-2876600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr7:2861400-2882200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr7:2861400-2883000	Weak transcription	Thymus	Thymus
7	chr7:2861800-2882400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:2862200-2882600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:2862800-2882400	Weak transcription	A549	lung
10	chr7:2863000-2878600	Weak transcription	Small Intestine	intestine
11	chr7:2863200-2876600	Weak transcription	HUVEC	blood vessel
12	chr7:2863800-2881600	Weak transcription	HMEC	breast
13	chr7:2864200-2881000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr7:2864200-2882800	Weak transcription	Esophagus	oesophagus
15	chr7:2864600-2875000	Weak transcription	Gastric	stomach
16	chr7:2864800-2877200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr7:2864800-2878600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:2864800-2881800	Weak transcription	Fetal Thymus	thymus
19	chr7:2865000-2877000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr7:2865000-2882400	Weak transcription	Fetal Kidney	kidney
21	chr7:2865200-2876600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr7:2865200-2877800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr7:2865200-2878600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr7:2865400-2877200	Weak transcription	Fetal Brain Male	brain
25	chr7:2865400-2877200	Weak transcription	Stomach Mucosa	stomach
26	chr7:2865400-2878600	Weak transcription	Brain Substantia Nigra	brain
27	chr7:2865400-2879600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr7:2865400-2882600	Weak transcription	HSMMtube	muscle
29	chr7:2865600-2880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr7:2865600-2883000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr7:2865800-2877000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:2867800-2877000	Strong transcription	Fetal Stomach	stomach
33	chr7:2868000-2877000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr7:2868200-2876600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr7:2868200-2877000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr7:2868600-2877000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr7:2868800-2876000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr7:2869200-2875000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr7:2869200-2875800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr7:2869200-2876600	Strong transcription	Fetal Muscle Leg	muscle
41	chr7:2869400-2876200	Strong transcription	Primary T cells from cord blood	blood
42	chr7:2869600-2877000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:2870400-2881400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr7:2871000-2878600	Weak transcription	Hela-S3	cervix
45	chr7:2871400-2875600	Strong transcription	Primary hematopoietic stem cells	blood
46	chr7:2871600-2875600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr7:2871600-2876200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:2871600-2876400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr7:2871800-2875200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr7:2871800-2877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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