Variant report

Variant	rs1111259
Chromosome Location	chr10:44821772-44821773
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	chr10:44810814..44813598-chr10:44820060..44822931,2	MCF-7	breast:
2	chr10:44821569..44823866-chr10:44836381..44838355,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11239000	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12240817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264745	0.86[YRI][hapmap]
rs12412586	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12414744	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1370158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1436931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17155986	1.00[CHB][hapmap]
rs1836982	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1898317	1.00[ASN][1000 genomes]
rs1898318	0.85[ASN][1000 genomes]
rs2028102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2118162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146807	0.82[MEX][hapmap]
rs2457481	1.00[ASN][1000 genomes]
rs2476351	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2505736	1.00[JPT][hapmap]
rs2505737	0.89[ASN][1000 genomes]
rs2505739	0.89[ASN][1000 genomes]
rs2505740	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2505743	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs266109	0.85[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2862116	1.00[CHB][hapmap]
rs56179443	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61856383	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61856384	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61856385	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72790834	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7894693	0.82[EUR][1000 genomes]
rs7915618	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7918046	0.93[YRI][hapmap]
rs977754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[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	nsv1038511	chr10:44596885-44870030	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1052337	chr10:44821390-44865015	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1111259	TMEM72	cis	cerebellum	SCAN
rs1111259	ZNF22	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44807200-44822200	Weak transcription	Left Ventricle	heart
2	chr10:44819400-44822400	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr10:44820000-44822200	Enhancers	HepG2	liver
4	chr10:44820000-44822400	Enhancers	Stomach Mucosa	stomach
5	chr10:44820000-44823000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr10:44820000-44823200	Enhancers	Pancreas	Pancrea
7	chr10:44820200-44821800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr10:44820400-44821800	Weak transcription	Fetal Thymus	thymus
9	chr10:44820600-44822400	Enhancers	Fetal Muscle Leg	muscle
10	chr10:44820600-44822400	Enhancers	Psoas Muscle	Psoas
11	chr10:44820800-44822400	Enhancers	Rectal Smooth Muscle	rectum
12	chr10:44820800-44822400	Enhancers	Right Atrium	heart
13	chr10:44820800-44822400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr10:44821000-44822400	Enhancers	Colon Smooth Muscle	Colon
15	chr10:44821200-44822000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr10:44821200-44822200	Weak transcription	Small Intestine	intestine
17	chr10:44821200-44822800	Enhancers	Fetal Heart	heart
18	chr10:44821400-44822000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr10:44821400-44822400	Enhancers	Right Ventricle	heart

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