Variant report

Variant	rs2250174
Chromosome Location	chr1:160950966-160950967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160945130..160946892-chr1:160950463..160952430,2	K562	blood:
2	chr1:160948860..160950429-chr1:160950620..160952705,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10737178	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs10908820	0.80[ASN][1000 genomes]
rs12132502	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2039223	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2184065	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2245672	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2246145	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2246484	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2246485	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2247472	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2249409	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2249933	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250304	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256505	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2256625	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2265239	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2265240	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2265242	0.89[AMR][1000 genomes]
rs2481073	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2481076	0.84[ASN][1000 genomes]
rs2481077	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2483139	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2483140	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2483141	0.92[CEU][hapmap];0.92[CHB][hapmap];0.87[YRI][hapmap]
rs2483142	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2779801	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2988722	0.83[AMR][1000 genomes]
rs2990694	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2990706	0.83[EUR][1000 genomes]
rs3007155	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4483427	0.96[ASN][1000 genomes]
rs6427563	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6427571	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6677526	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6677533	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7542911	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs790055	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs790056	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking 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	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2250174	F11R	cis	lymphoblastoid	seeQTL
rs2250174	F11R	cis	cerebellum	SCAN
rs2250174	TSTD1	cis	Adipose Subcutaneous	GTEx
rs2250174	F11R	cis	parietal	SCAN
rs2250174	NHLH1	cis	parietal	SCAN
rs2250174	TSTD1	cis	Nerve Tibial	GTEx
rs2250174	PAQR6	cis	cerebellum	SCAN
rs2250174	OR6K3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160943200-160951000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:160943200-160959800	Weak transcription	Pancreas	Pancrea
3	chr1:160948600-160968000	Weak transcription	Ovary	ovary
4	chr1:160950600-160951000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr1:160950600-160951400	Weak transcription	Right Atrium	heart
6	chr1:160950800-160951000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:160950800-160951000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr1:160950800-160951000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:160950800-160951000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
10	chr1:160950800-160951000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr1:160950800-160951000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
12	chr1:160950800-160951000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
13	chr1:160950800-160951200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:160950800-160951200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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