Variant report

Variant	rs4290029
Chromosome Location	chr1:224400640-224400641
allele	C/G
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	ZNF263	chr1:224400048-224400835	HEK293-T-REx	kidney:	n/a	n/a
2	GATA3	chr1:224400038-224400913	MCF-7	breast:	n/a	n/a
3	TCF7L2	chr1:224400225-224400930	MCF-7	breast:	n/a	chr1:224400524-224400538
4	TCF7L2	chr1:224400233-224400672	Hela-S3	cervix:	n/a	chr1:224400524-224400538
5	JUND	chr1:224400445-224400787	HepG2	liver:	n/a	chr1:224400624-224400635
6	FOSL2	chr1:224400394-224400812	HepG2	liver:	n/a	n/a
7	SIN3AK20	chr1:224400126-224400797	MCF-7	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NVL-1	chr1:224400457-224400981	XLOC_001225

Variant related genes	Relation type
ENSG00000232628	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10495222	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1060386	0.85[ASN][1000 genomes]
rs10753460	0.81[ASN][1000 genomes]
rs10799529	0.98[ASN][1000 genomes]
rs10799539	0.90[ASN][1000 genomes]
rs10799551	0.86[CHB][hapmap]
rs10916468	0.86[ASN][1000 genomes]
rs10916489	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10916512	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916515	0.94[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916533	0.83[ASN][1000 genomes]
rs10916534	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916535	0.83[ASN][1000 genomes]
rs11588603	0.82[ASN][1000 genomes]
rs11588981	0.85[ASN][1000 genomes]
rs12024159	0.84[ASN][1000 genomes]
rs12134258	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12135557	0.94[CHB][hapmap]
rs12142842	0.86[ASN][1000 genomes]
rs12143450	0.85[ASN][1000 genomes]
rs12143576	0.85[ASN][1000 genomes]
rs1401318	0.84[ASN][1000 genomes]
rs1533589	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs1976788	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2405302	0.91[ASN][1000 genomes]
rs4446934	0.86[ASN][1000 genomes]
rs4653997	0.86[ASN][1000 genomes]
rs4654009	0.86[CHB][hapmap]
rs4654010	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs55977521	0.86[ASN][1000 genomes]
rs56023673	0.82[ASN][1000 genomes]
rs6426060	0.84[ASN][1000 genomes]
rs6664230	0.86[CHB][hapmap]
rs6674695	0.92[ASN][1000 genomes]
rs6682662	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72753995	0.82[ASN][1000 genomes]
rs72755906	0.87[ASN][1000 genomes]
rs72755909	0.92[ASN][1000 genomes]
rs72755914	0.92[ASN][1000 genomes]
rs72755915	0.95[ASN][1000 genomes]
rs72755917	0.95[ASN][1000 genomes]
rs7541131	0.92[ASN][1000 genomes]
rs908802	0.86[ASN][1000 genomes]
rs908803	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs908804	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224389600-224414400	Weak transcription	Fetal Brain Female	brain
2	chr1:224391600-224407000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:224393600-224400800	Weak transcription	Right Atrium	heart
4	chr1:224393600-224401200	Weak transcription	Esophagus	oesophagus
5	chr1:224393600-224401200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:224393800-224405600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:224393800-224414200	Weak transcription	Colonic Mucosa	Colon
8	chr1:224394000-224400800	Weak transcription	HSMM	muscle
9	chr1:224394000-224401200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:224394000-224414000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:224394000-224414600	Weak transcription	HMEC	breast
12	chr1:224394400-224400800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:224396800-224402200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:224397000-224401800	Enhancers	Fetal Muscle Leg	muscle
15	chr1:224397600-224402200	Enhancers	Fetal Intestine Small	intestine
16	chr1:224397600-224402400	Enhancers	Stomach Mucosa	stomach
17	chr1:224397800-224402400	Enhancers	HepG2	liver
18	chr1:224398000-224401600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:224398000-224402400	Enhancers	Fetal Intestine Large	intestine
20	chr1:224398000-224414200	Weak transcription	Spleen	Spleen
21	chr1:224398200-224401200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:224398200-224401200	Weak transcription	GM12878-XiMat	blood
23	chr1:224398400-224401400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:224398600-224401800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr1:224398800-224401000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr1:224398800-224401400	Enhancers	Hela-S3	cervix
27	chr1:224398800-224401800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr1:224399000-224402200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:224399200-224402200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:224399400-224400800	Enhancers	Liver	Liver
31	chr1:224399400-224401400	Weak transcription	Left Ventricle	heart
32	chr1:224399400-224403600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr1:224399400-224406600	Weak transcription	Pancreas	Pancrea
34	chr1:224399400-224411000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:224399400-224414200	Weak transcription	Adipose Nuclei	Adipose
36	chr1:224399400-224414200	Weak transcription	Brain Anterior Caudate	brain
37	chr1:224399600-224401200	Weak transcription	Fetal Heart	heart
38	chr1:224399600-224401400	Weak transcription	Fetal Kidney	kidney
39	chr1:224399600-224401800	Enhancers	A549	lung
40	chr1:224399600-224405600	Weak transcription	Fetal Lung	lung
41	chr1:224400000-224401000	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr1:224400000-224401400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr1:224400000-224402000	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr1:224400200-224400800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:224400200-224401000	Enhancers	Gastric	stomach
46	chr1:224400200-224401000	Enhancers	HSMMtube	muscle
47	chr1:224400200-224401000	Flanking Active TSS	NHEK	skin
48	chr1:224400200-224401400	Enhancers	Fetal Muscle Trunk	muscle
49	chr1:224400200-224401400	Enhancers	Right Ventricle	heart
50	chr1:224400200-224401600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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