Variant report

Variant	rs1990354
Chromosome Location	chr7:139523858-139523859
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:139517568..139521373-chr7:139521587..139526613,5	K562	blood:
2	chr7:139521931..139523978-chr7:139621670..139623337,2	K562	blood:
3	chr7:139520823..139523874-chr7:139528601..139531758,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLEC2L-2	chr7:139523530-139525908	l_3489_NR_024451

Variant related genes	Relation type
ENSG00000059377	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10237429	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10253277	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10256282	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10257313	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs10277705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1074977	1.00[CHB][hapmap]
rs12534299	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs194152	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2079845	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs2107900	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2267679	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2361644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2361698	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4311593	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4590360	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4725857	0.85[GIH][hapmap]
rs4726776	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs4726815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4726838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727013	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56147462	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6464800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946849	0.85[ASN][1000 genomes]
rs6949027	1.00[CHB][hapmap]
rs6951759	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6952056	1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.85[ASN][1000 genomes]
rs6952322	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958644	1.00[CHB][hapmap]
rs6974960	0.85[ASN][1000 genomes]
rs6980375	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764745	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs764746	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7810415	0.83[GIH][hapmap]
rs9632668	0.87[CEU][hapmap]

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	nsv1020234	chr7:139377822-139661964	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1032711	chr7:139411404-139684043	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv464732	chr7:139424022-139654256	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv608472	chr7:139424022-139654256	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1018712	chr7:139429703-139658014	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv464733	chr7:139491967-139539218	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv608473	chr7:139491967-139539218	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:139517200-139529200	Weak transcription	Right Atrium	heart
2	chr7:139519200-139528200	Weak transcription	Gastric	stomach
3	chr7:139520600-139525600	Weak transcription	HMEC	breast
4	chr7:139523200-139524000	Enhancers	Fetal Lung	lung
5	chr7:139523200-139526400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:139523400-139524400	Enhancers	Colon Smooth Muscle	Colon
7	chr7:139523400-139524400	Bivalent Enhancer	NHLF	lung
8	chr7:139523400-139526200	Enhancers	Fetal Stomach	stomach
9	chr7:139523400-139526400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr7:139523600-139524000	Enhancers	Ovary	ovary
11	chr7:139523800-139524000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr7:139523800-139524000	Enhancers	HSMMtube	muscle
13	chr7:139523800-139524000	Enhancers	Osteobl	bone
14	chr7:139523800-139524200	Flanking Active TSS	Fetal Kidney	kidney
15	chr7:139523800-139526200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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