Variant report

Variant	rs10898929
Chromosome Location	chr11:73365695-73365696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10898926	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10898927	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898928	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235827	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11235834	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11235843	1.00[ASW][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11235864	1.00[ASW][hapmap]
rs11601905	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12361257	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12364069	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1568895	0.91[ASN][1000 genomes]
rs2272248	0.81[ASN][1000 genomes]
rs3741147	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3825003	1.00[ASW][hapmap]
rs4944032	1.00[ASW][hapmap]
rs4944847	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4944850	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944852	0.81[ASN][1000 genomes]
rs591804	0.80[GIH][hapmap]
rs650393	0.91[GIH][hapmap]
rs6590	1.00[ASW][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs666839	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7128512	0.84[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7939193	1.00[ASW][hapmap]
rs7944279	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9666549	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1045149	chr11:73314565-73581908	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv521125	chr11:73359236-73378142	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10898929	PAAF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73359000-73371600	Weak transcription	Fetal Brain Female	brain
2	chr11:73359000-73371600	Weak transcription	Right Ventricle	heart
3	chr11:73359200-73367200	Weak transcription	Spleen	Spleen
4	chr11:73359200-73371600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr11:73359200-73371600	Weak transcription	Thymus	Thymus
6	chr11:73359200-73371800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:73359400-73367000	Weak transcription	Lung	lung
8	chr11:73359400-73371800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr11:73359600-73372200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:73359800-73371800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr11:73359800-73371800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:73361400-73367800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr11:73361600-73365800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr11:73361800-73369200	Strong transcription	Primary T cells from cord blood	blood
15	chr11:73362000-73375000	Weak transcription	Aorta	Aorta
16	chr11:73362400-73366600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:73362800-73366600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:73362800-73367600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr11:73363400-73370400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr11:73363400-73371600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr11:73363600-73370400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr11:73363600-73371800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:73363800-73365800	Weak transcription	Fetal Intestine Large	intestine
24	chr11:73363800-73366000	Genic enhancers	Brain Angular Gyrus	brain
25	chr11:73363800-73366400	Genic enhancers	Brain Hippocampus Middle	brain
26	chr11:73363800-73366600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr11:73363800-73368000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr11:73363800-73371600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr11:73363800-73385400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr11:73364000-73366400	Genic enhancers	Brain Substantia Nigra	brain
31	chr11:73364000-73366600	Weak transcription	Pancreas	Pancrea
32	chr11:73364000-73371400	Weak transcription	Fetal Intestine Small	intestine
33	chr11:73364000-73371800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:73364200-73366600	Genic enhancers	HepG2	liver
35	chr11:73364400-73365800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:73364400-73366400	Weak transcription	Gastric	stomach
37	chr11:73364400-73368800	Weak transcription	Fetal Muscle Leg	muscle
38	chr11:73364400-73371400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:73364400-73371600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr11:73364400-73371800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr11:73364400-73371800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr11:73364600-73366000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:73364600-73371400	Weak transcription	Stomach Mucosa	stomach
44	chr11:73364600-73371600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr11:73364800-73366000	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr11:73364800-73371800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr11:73365000-73365800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr11:73365200-73366000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:73365200-73367000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:73365400-73366000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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