Variant report

Variant	rs11169407
Chromosome Location	chr12:39149497-39149498
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39148035..39150623-chr12:39154399..39156459,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1021256	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1021258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1038540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1038543	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10747574	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875959	1.00[JPT][hapmap]
rs10875962	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs10875963	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs1095577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169095	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11169333	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12309958	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12578804	1.00[CEU][hapmap]
rs12580606	1.00[CEU][hapmap]
rs1472657	1.00[EUR][1000 genomes]
rs1486346	0.89[AMR][1000 genomes]
rs1486348	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1486349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1486350	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1486351	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1486352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1486353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1615569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1619885	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];0.95[ASN][1000 genomes]
rs1620594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1620655	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1621467	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1624751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1684419	1.00[CEU][hapmap];0.97[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1684420	0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1684421	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17126226	1.00[CEU][hapmap]
rs1719846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1843640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1843641	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1847181	0.93[EUR][1000 genomes]
rs1906043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2101370	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs2388058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2653739	0.93[EUR][1000 genomes]
rs2730891	1.00[JPT][hapmap]
rs2730911	1.00[JPT][hapmap]
rs4293160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs4456302	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4494336	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4767968	1.00[EUR][1000 genomes]
rs5005131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs7297083	1.00[CEU][hapmap]
rs7957523	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs7971223	0.82[ASN][1000 genomes]
rs7976054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7978885	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs826842	1.00[CEU][hapmap]
rs826864	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs826878	0.90[JPT][hapmap]
rs826893	0.91[JPT][hapmap]
rs864324	0.91[JPT][hapmap];0.86[YRI][hapmap]
rs9645814	1.00[JPT][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
2	chr12:39092600-39153600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:39115800-39164400	Weak transcription	Lung	lung
4	chr12:39116000-39154800	Weak transcription	Aorta	Aorta
5	chr12:39118400-39165600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:39135800-39159000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:39139000-39153600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:39140600-39155000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:39141000-39155800	Weak transcription	Ovary	ovary
10	chr12:39141800-39153600	Weak transcription	Adipose Nuclei	Adipose
11	chr12:39142400-39154200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:39143800-39153200	Weak transcription	Liver	Liver
13	chr12:39144200-39163400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:39144200-39173800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:39144400-39152400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr12:39144400-39153600	Weak transcription	Left Ventricle	heart
17	chr12:39144600-39156200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:39145000-39153200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:39146000-39153600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:39146400-39165400	Weak transcription	GM12878-XiMat	blood
21	chr12:39149200-39150000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr12:39149200-39150800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:39149400-39150200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:39149400-39154800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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