Variant report

Variant	rs7946
Chromosome Location	chr17:17409560-17409561
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	chr17:17396995..17404908-chr17:17406815..17414609,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108551	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11652200	0.81[EUR][1000 genomes]
rs1242490	0.81[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs1242499	0.81[TSI][hapmap]
rs1242500	0.81[TSI][hapmap]
rs1242502	0.81[TSI][hapmap]
rs1242514	0.81[TSI][hapmap]
rs1242515	0.81[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs1242517	0.85[EUR][1000 genomes]
rs1242518	0.85[EUR][1000 genomes]
rs12938634	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1918249	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232831	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2694920	0.83[EUR][1000 genomes]
rs2694927	0.81[TSI][hapmap]
rs28435349	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3816511	0.83[AMR][1000 genomes]
rs4479310	0.91[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4646408	1.00[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4646410	0.87[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4924755	0.81[CEU][hapmap]
rs4924868	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4924890	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4924891	0.81[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7219976	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7220132	0.91[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7220217	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8074074	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8074191	0.85[CEU][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482648	chr17:17315268-17455442	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv907729	chr17:17338536-17425279	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv907730	chr17:17358004-17415217	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv907731	chr17:17358004-17504856	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv907732	chr17:17381764-17415217	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv907733	chr17:17381764-17422608	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv907734	chr17:17381764-17425858	Enhancers Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv907735	chr17:17381764-17448589	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv907736	chr17:17381764-17465458	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv907737	chr17:17388167-17411030	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv907738	chr17:17404586-17422608	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv907739	chr17:17404586-17424333	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv907740	chr17:17404586-17425858	Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv907741	chr17:17404586-17429927	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
15	nsv907742	chr17:17404586-17432744	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
16	nsv907743	chr17:17404586-17448589	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
17	nsv907744	chr17:17404586-17504856	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer 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 target site	12 gene(s)	inside rSNPs	diseases
18	nsv574524	chr17:17408484-17414594	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
19	esv1803680	chr17:17408484-17426009	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7946	TNFRSF13B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17399600-17413800	Weak transcription	Dnd41	blood
2	chr17:17400600-17409800	Weak transcription	Esophagus	oesophagus
3	chr17:17400600-17410000	Weak transcription	Liver	Liver
4	chr17:17400600-17415200	Weak transcription	Ovary	ovary
5	chr17:17400600-17422000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr17:17400800-17413000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr17:17400800-17419200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr17:17401000-17411200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:17401000-17418800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr17:17401000-17425400	Weak transcription	Thymus	Thymus
11	chr17:17401200-17411000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr17:17401200-17415200	Weak transcription	Gastric	stomach
13	chr17:17405600-17412000	Enhancers	Fetal Muscle Trunk	muscle
14	chr17:17405800-17413200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr17:17406200-17415800	Enhancers	Fetal Heart	heart
16	chr17:17406600-17414600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:17406800-17410600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:17407400-17409600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr17:17407400-17409800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:17407400-17409800	Weak transcription	Right Atrium	heart
21	chr17:17407400-17425400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr17:17407800-17418400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr17:17407800-17422600	Weak transcription	Brain Germinal Matrix	brain
24	chr17:17408000-17409600	Weak transcription	Brain Hippocampus Middle	brain
25	chr17:17408000-17409600	Strong transcription	Fetal Stomach	stomach
26	chr17:17408000-17410000	Weak transcription	Brain Anterior Caudate	brain
27	chr17:17408000-17410200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr17:17408000-17411200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr17:17408000-17418200	Weak transcription	Fetal Brain Female	brain
30	chr17:17408000-17418400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr17:17408200-17419200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr17:17408400-17409600	Weak transcription	Brain Angular Gyrus	brain
33	chr17:17408400-17409800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr17:17408400-17410000	Weak transcription	Fetal Brain Male	brain
35	chr17:17408400-17417600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr17:17408800-17414400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:17409000-17409600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr17:17409000-17410600	Enhancers	Right Ventricle	heart
39	chr17:17409000-17411400	Enhancers	Lung	lung
40	chr17:17409200-17410200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr17:17409200-17410400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:17409200-17411000	Enhancers	Adipose Nuclei	Adipose
43	chr17:17409200-17411800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr17:17409400-17411000	Genic enhancers	Fetal Intestine Small	intestine
45	chr17:17409400-17411000	Enhancers	Stomach Mucosa	stomach
46	chr17:17409400-17411400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr17:17409400-17411400	Enhancers	Spleen	Spleen
48	chr17:17409400-17411800	Enhancers	Fetal Muscle Leg	muscle

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