Variant report

Variant	rs7942963
Chromosome Location	chr11:73615599-73615600
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10501412	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs10898947	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs10898949	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11235898	0.82[ASN][1000 genomes]
rs11235905	0.82[ASN][1000 genomes]
rs11235907	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs11235908	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs11235910	0.82[ASN][1000 genomes]
rs11235913	0.82[ASN][1000 genomes]
rs11235914	0.82[ASN][1000 genomes]
rs11235915	0.82[ASN][1000 genomes]
rs11235920	1.00[YRI][hapmap]
rs11235922	1.00[JPT][hapmap]
rs11235925	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs11235927	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs11235931	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11235933	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11235934	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11235939	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11235947	0.89[ASN][1000 genomes]
rs12365080	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12420099	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12420751	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12421077	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12421900	0.83[ASN][1000 genomes]
rs17132369	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs17132397	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs17132403	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17132411	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1814547	0.83[ASN][1000 genomes]
rs1869433	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2067912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3741137	0.86[ASN][1000 genomes]
rs4537782	0.84[ASN][1000 genomes]
rs4944034	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs4944868	0.83[ASN][1000 genomes]
rs4944869	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs55910552	0.82[ASN][1000 genomes]
rs60020777	0.82[ASN][1000 genomes]
rs60812833	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60863026	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66610247	0.82[ASN][1000 genomes]
rs7119528	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs72982926	0.86[ASN][1000 genomes]
rs72982937	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs72989228	0.82[ASN][1000 genomes]
rs7929705	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1038105	chr11:73552023-73673836	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1035977	chr11:73581224-73617653	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7942963	PAAF1	Cis_1M	lymphoblastoid	RTeQTL
rs7942963	PAAF1	cis	multi-tissue	Pritchard
rs7942963	WDR71	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73588800-73622000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:73588800-73623000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr11:73588800-73625200	Weak transcription	Small Intestine	intestine
4	chr11:73588800-73630000	Weak transcription	Colonic Mucosa	Colon
5	chr11:73588800-73630200	Weak transcription	HUVEC	blood vessel
6	chr11:73589000-73630200	Weak transcription	Fetal Brain Male	brain
7	chr11:73589400-73629200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:73591600-73618000	Weak transcription	K562	blood
9	chr11:73596000-73640800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:73600400-73618000	Weak transcription	Fetal Heart	heart
11	chr11:73601000-73640400	Weak transcription	Stomach Mucosa	stomach
12	chr11:73601600-73630000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:73602000-73622800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:73602000-73624000	Weak transcription	Psoas Muscle	Psoas
15	chr11:73602400-73644800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr11:73604400-73623400	Weak transcription	Fetal Kidney	kidney
17	chr11:73605200-73618400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr11:73606600-73630000	Weak transcription	A549	lung
19	chr11:73606800-73638200	Weak transcription	NHLF	lung
20	chr11:73607200-73628400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:73610200-73616600	Strong transcription	Fetal Stomach	stomach
22	chr11:73610400-73618400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:73610400-73620200	Weak transcription	HMEC	breast
24	chr11:73611000-73628200	Weak transcription	Gastric	stomach
25	chr11:73611200-73628600	Weak transcription	Esophagus	oesophagus
26	chr11:73611600-73615800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr11:73611600-73616000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr11:73611600-73616200	Weak transcription	Colon Smooth Muscle	Colon
29	chr11:73611600-73618000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:73611600-73618200	Weak transcription	GM12878-XiMat	blood
31	chr11:73611600-73618400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:73611600-73618400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:73611600-73618400	Weak transcription	Lung	lung
34	chr11:73611600-73618400	Weak transcription	Right Ventricle	heart
35	chr11:73611600-73620200	Weak transcription	Brain Angular Gyrus	brain
36	chr11:73611600-73620200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr11:73611600-73620200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr11:73611600-73620400	Weak transcription	Brain Anterior Caudate	brain
39	chr11:73611600-73621800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr11:73611600-73622200	Weak transcription	Spleen	Spleen
41	chr11:73611600-73624800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr11:73611600-73624800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr11:73611600-73625000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr11:73611600-73627800	Weak transcription	NHDF-Ad	bronchial
45	chr11:73611600-73628600	Weak transcription	Aorta	Aorta
46	chr11:73611600-73630200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr11:73611800-73615800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr11:73611800-73618400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:73611800-73618400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:73611800-73618400	Weak transcription	Pancreas	Pancrea

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