Variant report

Variant	rs12745664
Chromosome Location	chr1:161370985-161370986
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:161370900-161372674	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161170920..161172634-chr1:161367719..161371418,3	K562	blood:
2	chr1:161194302..161197797-chr1:161367692..161371264,4	K562	blood:
3	chr1:161195417..161197356-chr1:161369111..161371418,2	MCF-7	breast:
4	chr1:161169854..161174151-chr1:161367669..161371061,6	K562	blood:
5	chr1:161284112..161286514-chr1:161369211..161371355,2	K562	blood:
6	chr1:161167864..161169396-chr1:161369052..161371683,2	MCF-7	breast:
7	chr1:161164912..161166810-chr1:161369417..161371024,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000215840	TF binding region
RNU6-481P	TF binding region
ENSG00000263548	Chromatin interaction
ENSG00000158859	Chromatin interaction
ENSG00000143252	Chromatin interaction
ENSG00000158864	Chromatin interaction
ENSG00000158882	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10494352	0.83[JPT][hapmap]
rs12745115	0.85[JPT][hapmap]
rs3813630	0.89[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs4077630	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4256831	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4282845	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4656297	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7515068	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530775	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432986	chr1:161221133-161673682	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1010776	chr1:161282384-161409218	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv432998	chr1:161335902-161673682	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv872493	chr1:161339060-161413794	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv433009	chr1:161343927-161639328	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
6	nsv1005812	chr1:161343951-161548101	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv535182	chr1:161343951-161548101	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
8	esv2756866	chr1:161344255-161681552	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
9	esv2758972	chr1:161344255-161681552	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
10	nsv998957	chr1:161353351-161398414	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
11	nsv433020	chr1:161355634-161673682	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
12	esv2754329	chr1:161355728-161673682	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
13	nsv433031	chr1:161355728-161673682	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12745664	OR6N2	cis	cerebellum	SCAN
rs12745664	OR10R2	cis	parietal	SCAN
rs12745664	NDUFS2	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161368400-161371000	Active TSS	Rectal Smooth Muscle	rectum
2	chr1:161368600-161371000	Active TSS	Brain Anterior Caudate	brain
3	chr1:161368600-161371000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr1:161369800-161371000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:161370200-161371000	Flanking Active TSS	Dnd41	blood
6	chr1:161370400-161371000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr1:161370400-161371000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr1:161370400-161371000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:161370400-161371000	Enhancers	Brain Angular Gyrus	brain
10	chr1:161370400-161371000	Enhancers	Fetal Intestine Large	intestine
11	chr1:161370400-161371000	Enhancers	Fetal Thymus	thymus
12	chr1:161370400-161371000	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr1:161370400-161371000	Enhancers	Spleen	Spleen
14	chr1:161370400-161371200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:161370400-161371400	Enhancers	Primary B cells from peripheral blood	blood
16	chr1:161370400-161375400	Weak transcription	Ovary	ovary
17	chr1:161370400-161379200	Weak transcription	Stomach Mucosa	stomach
18	chr1:161370400-161380000	Weak transcription	Gastric	stomach
19	chr1:161370600-161371000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:161370600-161371000	Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr1:161370600-161371000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:161370600-161371000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr1:161370600-161371000	Enhancers	Duodenum Mucosa	Duodenum
24	chr1:161370600-161371000	Enhancers	Fetal Intestine Small	intestine
25	chr1:161370600-161371000	Enhancers	Fetal Lung	lung
26	chr1:161370600-161371000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr1:161370600-161371000	Enhancers	Right Atrium	heart
28	chr1:161370600-161371000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:161370600-161371000	Flanking Active TSS	K562	blood
30	chr1:161370600-161371200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr1:161370600-161371200	Enhancers	Fetal Muscle Leg	muscle
32	chr1:161370600-161371200	Enhancers	HepG2	liver
33	chr1:161370600-161371400	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr1:161370600-161371800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:161370600-161371800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:161370600-161372000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:161370600-161372200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr1:161370600-161372200	Weak transcription	Lung	lung
39	chr1:161370600-161372200	Weak transcription	A549	lung
40	chr1:161370600-161372200	Weak transcription	Osteobl	bone
41	chr1:161370600-161372400	Enhancers	Pancreas	Pancrea
42	chr1:161370600-161372800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:161370600-161373600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:161370600-161373800	Weak transcription	Small Intestine	intestine
45	chr1:161370600-161375200	Weak transcription	Hela-S3	cervix
46	chr1:161370600-161378600	Weak transcription	Fetal Heart	heart
47	chr1:161370600-161381800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:161370800-161371000	Enhancers	H1 Cell Line	embryonic stem cell
49	chr1:161370800-161371000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr1:161370800-161371000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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