Variant report

Variant	rs599386
Chromosome Location	chr1:78638446-78638447
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	TCF12	chr1:78637241-78638495	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr1:78637327-78638503	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr1:78637250-78638555	SK-N-SH	brain:	n/a	n/a
4	EP300	chr1:78637247-78638507	SK-N-SH	brain:	n/a	n/a
5	JUND	chr1:78637305-78638473	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RNFT1P2	TF binding region

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10873966	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11162418	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162420	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162421	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162422	0.98[ASN][1000 genomes]
rs11162423	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11162425	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11584032	1.00[ASN][1000 genomes]
rs12082228	0.99[ASN][1000 genomes]
rs12083265	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12095545	0.84[EUR][1000 genomes]
rs12131414	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133075	0.95[ASN][1000 genomes]
rs12749252	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1323094	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1359043	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407747	0.86[ASN][1000 genomes]
rs1407748	0.86[ASN][1000 genomes]
rs1621088	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1625234	0.86[ASN][1000 genomes]
rs1770306	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1770307	0.90[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs1770313	0.81[AMR][1000 genomes]
rs2025610	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025611	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025612	0.96[ASN][1000 genomes]
rs2025613	0.95[ASN][1000 genomes]
rs2025614	0.96[ASN][1000 genomes]
rs2146612	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2208966	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2209472	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2351907	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2351909	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2351910	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882796	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2882797	0.98[ASN][1000 genomes]
rs2882798	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258183	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4258184	0.86[ASN][1000 genomes]
rs4268312	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285658	0.86[ASN][1000 genomes]
rs4396076	0.99[ASN][1000 genomes]
rs4529663	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4587522	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650313	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650315	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650382	0.89[CEU][hapmap]
rs4650607	0.84[ASN][1000 genomes]
rs488469	0.82[ASN][1000 genomes]
rs501774	0.82[ASN][1000 genomes]
rs513245	0.82[ASN][1000 genomes]
rs513977	0.82[ASN][1000 genomes]
rs561289	0.82[ASN][1000 genomes]
rs577978	0.83[JPT][hapmap]
rs581926	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs582795	0.85[ASN][1000 genomes]
rs584660	0.85[JPT][hapmap]
rs585100	0.83[JPT][hapmap]
rs58611517	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591343	0.83[ASN][1000 genomes]
rs596803	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs597063	0.83[ASN][1000 genomes]
rs597272	0.85[ASN][1000 genomes]
rs605659	0.86[JPT][hapmap]
rs60588097	0.91[ASN][1000 genomes]
rs610508	0.85[ASN][1000 genomes]
rs614963	0.85[JPT][hapmap]
rs616518	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61777350	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs618063	0.81[ASN][1000 genomes]
rs618551	0.82[ASN][1000 genomes]
rs618593	0.82[ASN][1000 genomes]
rs619749	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs624766	0.82[ASN][1000 genomes]
rs627493	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs627549	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs627661	0.85[JPT][hapmap]
rs633664	0.81[ASN][1000 genomes]
rs634741	0.85[ASN][1000 genomes]
rs637943	0.82[ASN][1000 genomes]
rs638232	0.80[EUR][1000 genomes]
rs640124	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs642248	0.83[JPT][hapmap]
rs6424716	1.00[ASN][1000 genomes]
rs6424717	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644332	0.84[ASN][1000 genomes]
rs649502	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs651413	0.88[ASN][1000 genomes]
rs653899	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs656372	0.82[ASN][1000 genomes]
rs658212	0.82[ASN][1000 genomes]
rs659902	0.85[ASN][1000 genomes]
rs663254	0.83[JPT][hapmap]
rs672391	0.82[ASN][1000 genomes]
rs675799	0.83[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs677875	0.83[ASN][1000 genomes]
rs680143	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs680971	0.83[ASN][1000 genomes]
rs683097	0.82[ASN][1000 genomes]
rs684657	0.95[ASN][1000 genomes]
rs684996	0.83[ASN][1000 genomes]
rs687708	0.85[JPT][hapmap]
rs688570	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs689374	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs699009	0.82[ASN][1000 genomes]
rs72688712	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7367729	0.97[ASN][1000 genomes]
rs7417073	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532752	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555504	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425188	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850497	chr1:78596312-78645701	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78625200-78644400	Weak transcription	Pancreas	Pancrea
2	chr1:78635000-78646200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:78636600-78638600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:78637000-78638600	Enhancers	HSMM	muscle
5	chr1:78637200-78638600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:78637200-78638600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:78637200-78638800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:78637200-78639400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr1:78637600-78638600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:78637600-78638600	Enhancers	HUVEC	blood vessel
11	chr1:78637600-78638600	Enhancers	NHDF-Ad	bronchial
12	chr1:78638000-78638600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:78638000-78638600	Enhancers	NHEK	skin
14	chr1:78638000-78638600	Enhancers	Osteobl	bone
15	chr1:78638000-78638800	Enhancers	HMEC	breast
16	chr1:78638200-78638600	Enhancers	NH-A	brain
17	chr1:78638400-78638600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:78638400-78638800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr1:78638400-78641800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:78638400-78641800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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