Variant report

Variant	rs11899711
Chromosome Location	chr2:151502215-151502216
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10186504	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10188741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10196763	0.89[EUR][1000 genomes]
rs10201751	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10432416	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497064	0.98[ASN][1000 genomes]
rs10497067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497069	1.00[AFR][1000 genomes]
rs10803803	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10930198	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10930203	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052383	0.81[CHB][hapmap]
rs12473120	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12614085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13019271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416697	0.90[EUR][1000 genomes]
rs13421850	0.90[EUR][1000 genomes]
rs13430342	0.90[EUR][1000 genomes]
rs1519782	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16828368	0.81[CHB][hapmap]
rs16828577	0.89[EUR][1000 genomes]
rs2247416	0.98[ASN][1000 genomes]
rs2290815	0.98[ASN][1000 genomes]
rs2290816	0.98[ASN][1000 genomes]
rs2341059	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs2341060	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341061	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341062	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2341063	0.98[ASN][1000 genomes]
rs2341064	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2341065	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2341066	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2341067	0.95[ASN][1000 genomes]
rs2341068	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2341071	0.98[ASN][1000 genomes]
rs2341072	0.93[ASN][1000 genomes]
rs2341073	0.95[ASN][1000 genomes]
rs2341074	0.98[ASN][1000 genomes]
rs2341075	0.93[ASN][1000 genomes]
rs2341078	0.98[ASN][1000 genomes]
rs2341081	0.98[ASN][1000 genomes]
rs2341082	0.98[ASN][1000 genomes]
rs2341083	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341084	0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341085	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341086	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341087	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2341088	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341090	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879931	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2879932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4233665	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4233666	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4233667	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4297879	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4334493	0.81[CHB][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4365460	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4380232	0.98[ASN][1000 genomes]
rs4408725	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4514872	0.98[ASN][1000 genomes]
rs4530365	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4530366	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4600650	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4627564	0.94[AFR][1000 genomes]
rs4664150	0.98[ASN][1000 genomes]
rs4664689	1.00[ASW][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4664692	0.98[ASN][1000 genomes]
rs6710003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71338158	0.81[ASN][1000 genomes]
rs7557930	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7559963	0.82[ASN][1000 genomes]
rs7560326	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7562436	0.98[ASN][1000 genomes]
rs7569499	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7593427	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7597424	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7602198	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9287861	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9287862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1001838	chr2:150819672-151745876	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv535980	chr2:150819672-151745876	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv532473	chr2:151164210-151701860	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv834415	chr2:151374254-151558649	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv2757836	chr2:151457277-151844210	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv2759096	chr2:151457277-151844210	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11899711	SH2D2A	trans	brain	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:151494600-151504600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:151499000-151503600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:151499800-151502800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:151500000-151502400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:151500200-151502400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:151500400-151502600	Enhancers	Osteobl	bone
7	chr2:151500600-151502400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:151500800-151502600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:151501000-151503800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:151501400-151502400	Enhancers	NHDF-Ad	bronchial
11	chr2:151501600-151503600	Weak transcription	A549	lung
12	chr2:151501600-151519400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:151501800-151503400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:151502200-151503400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:151502200-151503400	Weak transcription	NHLF	lung
16	chr2:151502200-151504400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:151502200-151505200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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