Variant report

Variant	rs41301111
Chromosome Location	chr10:49456880-49456881
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:49455171..49457750-chr10:49459859..49462154,2	K562	blood:
2	chr10:49455171..49459058-chr10:49459196..49462154,3	K562	blood:
3	chr10:49455241..49456959-chr10:49462949..49465290,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPN20C-7	chr10:49456586-49457221	NONHSAT013263

Variant related genes	Relation type
ENSG00000170324	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1542153	1.00[EUR][1000 genomes]
rs1550774	1.00[EUR][1000 genomes]
rs2590379	1.00[EUR][1000 genomes]
rs2590380	1.00[EUR][1000 genomes]
rs2698765	1.00[EUR][1000 genomes]
rs3730154	1.00[EUR][1000 genomes]
rs4141840	1.00[EUR][1000 genomes]
rs59377405	1.00[EUR][1000 genomes]
rs60467447	1.00[EUR][1000 genomes]
rs61343950	1.00[EUR][1000 genomes]
rs7072065	1.00[EUR][1000 genomes]
rs7073628	1.00[EUR][1000 genomes]
rs73293121	1.00[EUR][1000 genomes]
rs73293181	1.00[EUR][1000 genomes]
rs73293198	1.00[EUR][1000 genomes]
rs73298383	1.00[EUR][1000 genomes]
rs73300395	1.00[EUR][1000 genomes]
rs74130210	0.83[EUR][1000 genomes]
rs74130211	0.87[AFR][1000 genomes]
rs74130215	0.87[AFR][1000 genomes]
rs74130216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7901179	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895367	chr10:49333754-49491047	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv895370	chr10:49421173-49484698	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49450800-49459400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr10:49451600-49459200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:49451800-49458200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:49451800-49459400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr10:49452000-49459400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr10:49454600-49457600	Enhancers	Right Ventricle	heart
7	chr10:49454800-49457800	Enhancers	Fetal Heart	heart
8	chr10:49455600-49458400	Enhancers	Fetal Thymus	thymus
9	chr10:49455800-49457000	Weak transcription	Left Ventricle	heart
10	chr10:49455800-49459400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr10:49456200-49457000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:49456200-49457000	Weak transcription	Right Atrium	heart
13	chr10:49456800-49457000	Enhancers	GM12878-XiMat	blood
14	chr10:49456800-49458000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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