Variant report

Variant	rs62198604
Chromosome Location	chr2:187229737-187229738
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZSWIM2-3	chr2:187229171-187229856	NONHSAT075981
2	lnc-ZSWIM2-3	chr2:187228431-187229856	NONHSAT075991

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10164423	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170460	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175904	0.85[EUR][1000 genomes]
rs10178380	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10188935	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189873	0.89[EUR][1000 genomes]
rs10190643	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199590	1.00[ASN][1000 genomes]
rs10201678	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202753	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202978	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206285	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208050	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208364	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208438	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383146	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13384032	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389341	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389837	0.85[EUR][1000 genomes]
rs13390957	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13391318	0.89[EUR][1000 genomes]
rs13396881	0.96[EUR][1000 genomes]
rs13398061	0.89[EUR][1000 genomes]
rs13398442	0.89[EUR][1000 genomes]
rs13398794	1.00[ASN][1000 genomes]
rs13400819	1.00[ASN][1000 genomes]
rs13404172	0.94[EUR][1000 genomes]
rs13411835	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13413555	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13414293	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13414549	0.94[EUR][1000 genomes]
rs13418456	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13421613	0.94[EUR][1000 genomes]
rs13424471	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13430022	1.00[ASN][1000 genomes]
rs16827613	0.89[EUR][1000 genomes]
rs16827842	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804162	0.94[EUR][1000 genomes]
rs36103051	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55908314	0.89[EUR][1000 genomes]
rs60597870	1.00[ASN][1000 genomes]
rs62197162	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197163	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197188	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197190	0.89[EUR][1000 genomes]
rs62197191	0.83[EUR][1000 genomes]
rs62197192	0.89[EUR][1000 genomes]
rs62197196	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197197	0.94[EUR][1000 genomes]
rs62197200	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197201	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197202	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197203	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197214	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197216	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197217	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197218	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197222	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197223	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197225	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs62197226	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197227	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197253	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197255	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62197257	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62198560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62198605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62198606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62198607	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62198611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62198612	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62198652	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62198656	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62198658	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62198659	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62199047	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62199048	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62199460	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62199522	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62199523	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62199524	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62199527	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62200577	1.00[ASN][1000 genomes]
rs62200580	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62200581	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62200583	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62200584	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979177	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979185	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73980894	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875545	chr2:186566024-187280164	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv868949	chr2:186657142-187327560	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv932296	chr2:186737443-187265790	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1006411	chr2:187150025-187291081	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv536079	chr2:187150025-187291081	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv428067	chr2:187171324-187334779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv961744	chr2:187189976-187265519	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv3071	chr2:187208040-187252682	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187214400-187239400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:187220400-187231800	Weak transcription	GM12878-XiMat	blood
3	chr2:187223600-187230800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:187226000-187232800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:187226400-187234000	Weak transcription	Left Ventricle	heart
6	chr2:187229400-187230000	Enhancers	Ovary	ovary
7	chr2:187229600-187229800	Enhancers	Aorta	Aorta
8	chr2:187229600-187230000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:187229600-187230000	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links