Variant report

Variant	rs2273712
Chromosome Location	chr1:241767708-241767709
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr1:241766947-241767838	PANC-1	pancreas:	n/a	chr1:241767401-241767410
2	JUND	chr1:241766074-241767772	SK-N-SH	brain:	n/a	chr1:241767400-241767411 chr1:241767401-241767411 chr1:241767401-241767410 chr1:241767401-241767411
3	TCF12	chr1:241767157-241767712	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr1:241767668-241767733	Lung_OC	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:241767091..241768658-chr1:242019786..242021766,2	K562	blood:
2	chr1:241760186..241764464-chr1:241765135..241770087,5	K562	blood:

Variant related genes	Relation type
OPN3	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11586782	1.00[AFR][1000 genomes]
rs11587755	1.00[AFR][1000 genomes]
rs11590381	1.00[AFR][1000 genomes]
rs12072790	1.00[MEX][hapmap]
rs12562746	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12568853	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841866	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2273710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41269375	1.00[AFR][1000 genomes]
rs45614438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56176170	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription 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	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241740400-241768800	Weak transcription	Spleen	Spleen
2	chr1:241743200-241768600	Weak transcription	Esophagus	oesophagus
3	chr1:241746600-241779200	Weak transcription	Lung	lung
4	chr1:241746800-241779600	Weak transcription	Aorta	Aorta
5	chr1:241750600-241771600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:241750600-241786000	Weak transcription	Fetal Brain Female	brain
7	chr1:241750800-241768800	Weak transcription	Fetal Kidney	kidney
8	chr1:241750800-241771800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:241750800-241773400	Weak transcription	Brain Angular Gyrus	brain
10	chr1:241750800-241774600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:241750800-241786200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:241752600-241773400	Weak transcription	Gastric	stomach
13	chr1:241753400-241791200	Weak transcription	Thymus	Thymus
14	chr1:241754200-241773600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:241754400-241782600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:241755000-241777600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:241755600-241773000	Weak transcription	Brain Germinal Matrix	brain
18	chr1:241755800-241775800	Weak transcription	Adipose Nuclei	Adipose
19	chr1:241756000-241769200	Weak transcription	Psoas Muscle	Psoas
20	chr1:241756000-241771000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:241756000-241791000	Weak transcription	Fetal Thymus	thymus
22	chr1:241756400-241773400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:241756400-241774600	Weak transcription	Small Intestine	intestine
24	chr1:241756400-241779000	Weak transcription	Colonic Mucosa	Colon
25	chr1:241756800-241771600	Weak transcription	NHLF	lung
26	chr1:241756800-241773000	Weak transcription	Pancreas	Pancrea
27	chr1:241758000-241777800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:241758000-241790800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:241758000-241797200	Weak transcription	Left Ventricle	heart
30	chr1:241758000-241800200	Weak transcription	Ovary	ovary
31	chr1:241758200-241771600	Weak transcription	HUVEC	blood vessel
32	chr1:241758400-241769000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:241758800-241772600	Weak transcription	Fetal Stomach	stomach
34	chr1:241758800-241778000	Weak transcription	Fetal Intestine Large	intestine
35	chr1:241758800-241802400	Weak transcription	Right Ventricle	heart
36	chr1:241759000-241790600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:241760400-241771800	Weak transcription	K562	blood
38	chr1:241760600-241773400	Weak transcription	Fetal Intestine Small	intestine
39	chr1:241761000-241772400	Weak transcription	Hela-S3	cervix
40	chr1:241764400-241771800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:241764400-241771800	Weak transcription	Brain Anterior Caudate	brain
42	chr1:241764600-241771800	Weak transcription	GM12878-XiMat	blood
43	chr1:241764600-241781400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:241765200-241767800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:241765200-241767800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:241765200-241768000	Strong transcription	Primary T cells from cord blood	blood
47	chr1:241765400-241768000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:241765400-241768000	Strong transcription	Placenta	Placenta
49	chr1:241765400-241769000	Strong transcription	Primary B cells from cord blood	blood
50	chr1:241765600-241769400	Strong transcription	Primary B cells from peripheral blood	blood

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