Variant report

Variant	rs12996417
Chromosome Location	chr2:9885391-9885392
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	NR3C1	chr2:9885265-9885668	A549	lung:	n/a	n/a
2	ZKSCAN1	chr2:9885364-9885717	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:9877830..9880619-chr2:9884575..9886353,2	MCF-7	breast:
2	chr2:9877832..9879861-chr2:9884355..9886742,3	K562	blood:

Variant related genes	Relation type
RNU4-73P	TF binding region
ENSG00000240960	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10171491	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10173057	0.90[ASN][1000 genomes]
rs10176382	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10178017	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10180724	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10200779	0.92[ASN][1000 genomes]
rs10200869	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10202283	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10929607	0.85[ASN][1000 genomes]
rs10929608	0.85[ASN][1000 genomes]
rs10929609	0.85[ASN][1000 genomes]
rs1110317	0.86[ASN][1000 genomes]
rs1123269	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11674024	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11676286	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11678697	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12470409	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12475853	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12476199	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12476232	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12692393	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12692394	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13018695	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13023725	0.81[ASN][1000 genomes]
rs13028425	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13395171	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13398163	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13398193	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13398304	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1554107	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1554108	0.83[ASN][1000 genomes]
rs34491197	0.82[ASN][1000 genomes]
rs4668644	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4669447	0.85[ASN][1000 genomes]
rs4669448	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4669451	0.84[ASN][1000 genomes]
rs6708081	0.84[ASN][1000 genomes]
rs6713497	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6732548	0.80[ASN][1000 genomes]
rs6740013	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6742929	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6743152	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6754662	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6756567	0.91[ASN][1000 genomes]
rs6761286	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6761920	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7423455	0.90[ASN][1000 genomes]
rs7423458	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs868442	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1014911	chr2:9863969-9905959	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9880200-9892800	Weak transcription	Thymus	Thymus
2	chr2:9880200-9893200	Weak transcription	Right Atrium	heart
3	chr2:9883600-9885400	Enhancers	Fetal Muscle Leg	muscle
4	chr2:9883800-9885400	Enhancers	Fetal Muscle Trunk	muscle
5	chr2:9884000-9885800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:9884000-9886000	Enhancers	NHDF-Ad	bronchial
7	chr2:9884200-9885400	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr2:9884200-9885600	Enhancers	Fetal Intestine Large	intestine
9	chr2:9884200-9885600	Enhancers	A549	lung
10	chr2:9884200-9886400	Enhancers	Pancreas	Pancrea
11	chr2:9884400-9885400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
12	chr2:9884400-9885400	Enhancers	Left Ventricle	heart
13	chr2:9884400-9885600	Enhancers	Lung	lung
14	chr2:9884400-9885600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr2:9884600-9885400	Bivalent Enhancer	HepG2	liver
16	chr2:9884600-9885600	Enhancers	HSMM	muscle
17	chr2:9884600-9885800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:9884600-9886600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:9884800-9885400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr2:9884800-9885600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:9884800-9885600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr2:9884800-9892600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:9885000-9885400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:9885000-9885400	Enhancers	Hela-S3	cervix
25	chr2:9885000-9885600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:9885000-9885600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:9885000-9885600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:9885000-9885600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:9885000-9885600	Enhancers	HMEC	breast
30	chr2:9885200-9885400	Enhancers	Psoas Muscle	Psoas
31	chr2:9885200-9885400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr2:9885200-9885600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:9885200-9885800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:9885200-9885800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:9885200-9886200	Weak transcription	Fetal Heart	heart
36	chr2:9885200-9888400	Weak transcription	Fetal Intestine Small	intestine
37	chr2:9885200-9891200	Weak transcription	Right Ventricle	heart
38	chr2:9885200-9891400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr2:9885200-9893000	Weak transcription	Rectal Mucosa Donor 29	rectum

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