Variant report

Variant	rs2740760
Chromosome Location	chr17:46643389-46643390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46618670..46620938-chr17:46642193..46644005,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230148	Chromatin interaction
ENSG00000173917	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11079828	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs11079830	0.86[JPT][hapmap]
rs11652860	0.83[AFR][1000 genomes]
rs2326013	0.84[ASN][1000 genomes]
rs2555111	0.84[TSI][hapmap];1.00[YRI][hapmap]
rs4793579	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4793927	0.82[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs9299	0.82[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
3	nsv908577	chr17:46584900-46704536	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	343 gene(s)	inside rSNPs	diseases
4	nsv908578	chr17:46592413-46698710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
5	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
6	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
7	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
8	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
9	nsv908580	chr17:46609103-46698710	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
10	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
11	nsv575480	chr17:46617019-46684929	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
12	nsv908582	chr17:46617019-46698710	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
13	nsv908583	chr17:46617019-46704536	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
14	nsv833471	chr17:46617787-46783345	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	356 gene(s)	inside rSNPs	diseases
15	nsv908584	chr17:46618926-46735520	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
16	nsv457822	chr17:46620402-46698710	Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
17	nsv575481	chr17:46620402-46698710	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
18	nsv457823	chr17:46620402-46704536	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
19	nsv575482	chr17:46620402-46704536	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
20	nsv457824	chr17:46625519-46693491	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
21	nsv575483	chr17:46625519-46693491	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
22	esv1007307	chr17:46638901-46653131	Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2740760	HOXB3	cis	Whole Blood	GTEx
rs2740760	HOXB-AS1	cis	Whole Blood	GTEx
rs2740760	RUNDC3A	cis	parietal	SCAN
rs2740760	HOXB2	Cis_1M	lymphoblastoid	RTeQTL
rs2740760	HOXB2	cis	Whole Blood	GTEx
rs2740760	ACLY	cis	parietal	SCAN
rs2740760	DUSP3	cis	cerebellum	SCAN
rs2740760	MPP2	cis	cerebellum	SCAN
rs2740760	PNPO	cis	parietal	SCAN
rs2740760	C17orf46	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46635000-46654600	Weak transcription	Hela-S3	cervix
2	chr17:46638000-46643800	Enhancers	Primary hematopoietic stem cells	blood
3	chr17:46639800-46648600	Weak transcription	Gastric	stomach
4	chr17:46640000-46645600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr17:46640400-46643800	Weak transcription	A549	lung
6	chr17:46641000-46643400	Weak transcription	K562	blood
7	chr17:46641200-46649000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
8	chr17:46641400-46643600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr17:46642000-46643400	Transcr. at gene 5' and 3'	NHLF	lung
10	chr17:46642200-46645000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:46642200-46647400	Weak transcription	Aorta	Aorta
12	chr17:46642400-46643400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
13	chr17:46642400-46643400	Bivalent Enhancer	Fetal Intestine Large	intestine
14	chr17:46642400-46643400	Enhancers	Placenta Amnion	Placenta Amnion
15	chr17:46642400-46643400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr17:46642400-46643600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr17:46642400-46643600	Genic enhancers	Rectal Mucosa Donor 29	rectum
18	chr17:46642400-46643600	Enhancers	Rectal Smooth Muscle	rectum
19	chr17:46642400-46643800	Weak transcription	Right Atrium	heart
20	chr17:46642400-46645000	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr17:46642400-46645800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:46642400-46645800	Bivalent Enhancer	Fetal Intestine Small	intestine
23	chr17:46642400-46646000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
24	chr17:46642400-46646600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr17:46642600-46643400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr17:46642600-46643800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
27	chr17:46642600-46644600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr17:46642600-46644600	Enhancers	Spleen	Spleen
29	chr17:46642600-46644800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
30	chr17:46642600-46644800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr17:46642600-46644800	Enhancers	Adipose Nuclei	Adipose
32	chr17:46642600-46645200	Genic enhancers	Fetal Stomach	stomach
33	chr17:46642800-46643600	Genic enhancers	HUVEC	blood vessel
34	chr17:46642800-46644600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr17:46642800-46645400	Enhancers	NHDF-Ad	bronchial
36	chr17:46642800-46645600	Genic enhancers	Fetal Kidney	kidney
37	chr17:46642800-46645800	Enhancers	Colonic Mucosa	Colon
38	chr17:46642800-46647400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr17:46642800-46647800	Weak transcription	HSMM	muscle
40	chr17:46643000-46643600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
41	chr17:46643000-46644800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr17:46643000-46644800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr17:46643000-46646200	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr17:46643200-46643400	Genic enhancers	Esophagus	oesophagus
45	chr17:46643200-46643600	Genic enhancers	Colon Smooth Muscle	Colon
46	chr17:46643200-46643800	Enhancers	Small Intestine	intestine
47	chr17:46643200-46644000	Flanking Bivalent TSS/Enh	Fetal Lung	lung
48	chr17:46643200-46645000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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