Variant report

Variant	rs56912118
Chromosome Location	chr17:16918076-16918077
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16917707..16920531-chr17:16944662..16947361,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNFRSF13B-2	chr17:16915228-16918304	ENSG00000260328.1

Variant related genes	Relation type
ENSG00000133030	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10048152	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1131632	1.00[EUR][1000 genomes]
rs16961406	1.00[EUR][1000 genomes]
rs28829096	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4485421	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55792503	1.00[EUR][1000 genomes]
rs56247606	1.00[EUR][1000 genomes]
rs56332804	0.93[AMR][1000 genomes]
rs56343767	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58169814	1.00[EUR][1000 genomes]
rs58442149	1.00[EUR][1000 genomes]
rs58690840	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58702370	1.00[EUR][1000 genomes]
rs59100652	0.93[AMR][1000 genomes]
rs60029796	1.00[EUR][1000 genomes]
rs60192272	1.00[EUR][1000 genomes]
rs60332371	1.00[EUR][1000 genomes]
rs60364428	1.00[EUR][1000 genomes]
rs60545734	1.00[EUR][1000 genomes]
rs60697210	1.00[EUR][1000 genomes]
rs60890438	1.00[EUR][1000 genomes]
rs61024568	1.00[EUR][1000 genomes]
rs61218165	1.00[EUR][1000 genomes]
rs61608940	1.00[EUR][1000 genomes]
rs7219836	1.00[EUR][1000 genomes]
rs7223145	1.00[EUR][1000 genomes]
rs7223758	1.00[EUR][1000 genomes]
rs73979025	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979028	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979045	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979046	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979048	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979049	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979056	1.00[EUR][1000 genomes]
rs73979057	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979063	1.00[EUR][1000 genomes]
rs73979079	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73979080	1.00[EUR][1000 genomes]
rs73979085	0.85[AMR][1000 genomes]
rs73979088	1.00[EUR][1000 genomes]
rs73979096	1.00[EUR][1000 genomes]
rs73979097	1.00[EUR][1000 genomes]
rs73981903	1.00[EUR][1000 genomes]
rs73981904	1.00[EUR][1000 genomes]
rs8064771	0.86[AMR][1000 genomes]
rs8069049	0.81[AMR][1000 genomes]
rs8079021	1.00[EUR][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	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv2761948	chr17:16868561-16920568	Weak transcription Enhancers Active TSS Flanking Active TSS 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	10 gene(s)	inside rSNPs	diseases
5	nsv907727	chr17:16892265-16938582	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv962271	chr17:16912264-16922846	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16903200-16921000	Weak transcription	Lung	lung
2	chr17:16905800-16920000	Weak transcription	Fetal Intestine Large	intestine
3	chr17:16906800-16923400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr17:16913600-16918600	Weak transcription	Pancreas	Pancrea
5	chr17:16913600-16921000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr17:16914800-16918600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr17:16914800-16919000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:16915000-16923600	Weak transcription	HSMMtube	muscle
9	chr17:16915200-16920000	Weak transcription	Fetal Intestine Small	intestine
10	chr17:16917400-16918800	Flanking Active TSS	Hela-S3	cervix
11	chr17:16917400-16919000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr17:16917400-16919200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr17:16917400-16919400	Enhancers	NHEK	skin
14	chr17:16917400-16920200	Enhancers	HMEC	breast
15	chr17:16917400-16922000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr17:16917400-16923800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:16917400-16926200	Enhancers	Stomach Mucosa	stomach
18	chr17:16917600-16918200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:16917600-16918200	Active TSS	Brain Anterior Caudate	brain
20	chr17:16917600-16918600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr17:16917600-16918600	Enhancers	HUVEC	blood vessel
22	chr17:16917600-16918600	Enhancers	NH-A	brain
23	chr17:16917600-16918600	Enhancers	Osteobl	bone
24	chr17:16917600-16919000	Enhancers	Esophagus	oesophagus
25	chr17:16917600-16919000	Enhancers	Gastric	stomach
26	chr17:16917800-16918200	Enhancers	Duodenum Mucosa	Duodenum
27	chr17:16917800-16918600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:16918000-16918400	Flanking Active TSS	A549	lung
29	chr17:16918000-16918800	Enhancers	HSMM	muscle
30	chr17:16918000-16922000	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr17:16918000-16922000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr17:16918000-16926200	Enhancers	Placenta	Placenta

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