Variant report

Variant	rs12108985
Chromosome Location	chr5:7907309-7907310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11949523	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13154459	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13178414	0.92[CEU][hapmap]
rs13181011	1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs13189728	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13190084	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17184211	1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17243407	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17245023	0.89[EUR][1000 genomes]
rs17267737	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2128266	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34966478	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62342527	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62342530	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7716373	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9282787	1.00[CEU][hapmap];0.94[AMR][1000 genomes];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	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv597005	chr5:7860404-8093077	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv427707	chr5:7866234-7966019	Strong transcription Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv508345	chr5:7890892-7933471	Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7871800-7907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:7874000-7909200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr5:7878600-7911800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:7895400-7909600	Weak transcription	Fetal Heart	heart
5	chr5:7899600-7910000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:7899600-7912000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:7899800-7909200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr5:7899800-7909200	Weak transcription	Esophagus	oesophagus
9	chr5:7900000-7909600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:7900000-7914600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:7900600-7909200	Weak transcription	Gastric	stomach
12	chr5:7902200-7909000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr5:7902400-7907800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr5:7902400-7907800	Weak transcription	Psoas Muscle	Psoas
15	chr5:7902400-7909000	Weak transcription	Aorta	Aorta
16	chr5:7902400-7909000	Weak transcription	Right Ventricle	heart
17	chr5:7902400-7909000	Weak transcription	K562	blood
18	chr5:7902400-7910200	Weak transcription	Fetal Brain Male	brain
19	chr5:7902400-7910800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:7902400-7911200	Weak transcription	Fetal Kidney	kidney
21	chr5:7902800-7907600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr5:7902800-7911200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:7903400-7907400	Weak transcription	Brain Substantia Nigra	brain
24	chr5:7903400-7908200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:7903400-7908200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr5:7903400-7909000	Weak transcription	Colonic Mucosa	Colon
27	chr5:7903400-7909200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:7903400-7911000	Weak transcription	Fetal Thymus	thymus
29	chr5:7903600-7908200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr5:7903600-7909000	Weak transcription	Brain Angular Gyrus	brain
31	chr5:7903600-7909200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:7903600-7916000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:7903800-7907600	Weak transcription	GM12878-XiMat	blood
34	chr5:7903800-7907800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr5:7903800-7913600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr5:7904000-7907600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:7904000-7907600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr5:7904000-7907800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr5:7904000-7908000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr5:7904000-7908800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:7904000-7909000	Weak transcription	Lung	lung
42	chr5:7904000-7909000	Weak transcription	Spleen	Spleen
43	chr5:7904000-7911400	Weak transcription	Small Intestine	intestine
44	chr5:7904200-7907400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr5:7904200-7907800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:7904200-7909000	Weak transcription	Placenta	Placenta
47	chr5:7904200-7909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr5:7904200-7909800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:7904200-7910800	Weak transcription	Thymus	Thymus
50	chr5:7904200-7912000	Weak transcription	Pancreas	Pancrea

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