Variant report

Variant	rs56241824
Chromosome Location	chr2:10069327-10069328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10803707	0.88[AFR][1000 genomes]
rs10803709	0.88[AFR][1000 genomes]
rs10803710	0.88[AFR][1000 genomes]
rs10929620	0.84[AFR][1000 genomes]
rs10929621	0.88[AFR][1000 genomes]
rs12465661	0.84[AFR][1000 genomes]
rs12466497	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12468764	0.88[AFR][1000 genomes]
rs12473944	0.84[AFR][1000 genomes]
rs12477755	0.93[EUR][1000 genomes]
rs12623211	0.84[AFR][1000 genomes]
rs12623217	0.82[AFR][1000 genomes]
rs12991487	0.85[AFR][1000 genomes]
rs1709854	0.92[EUR][1000 genomes]
rs17364189	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241664	0.93[EUR][1000 genomes]
rs34153848	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34577787	0.88[AFR][1000 genomes]
rs35029226	0.88[EUR][1000 genomes]
rs369551	0.90[EUR][1000 genomes]
rs369605	0.90[EUR][1000 genomes]
rs371305	0.92[EUR][1000 genomes]
rs372031	0.92[EUR][1000 genomes]
rs374197	0.92[EUR][1000 genomes]
rs375793	0.90[EUR][1000 genomes]
rs386355	0.90[EUR][1000 genomes]
rs388695	0.88[EUR][1000 genomes]
rs389002	0.88[EUR][1000 genomes]
rs391889	0.92[EUR][1000 genomes]
rs395381	0.89[EUR][1000 genomes]
rs396281	0.89[EUR][1000 genomes]
rs397498	0.90[EUR][1000 genomes]
rs397871	0.90[EUR][1000 genomes]
rs400758	0.92[EUR][1000 genomes]
rs403317	0.90[EUR][1000 genomes]
rs407874	0.90[EUR][1000 genomes]
rs408987	0.92[EUR][1000 genomes]
rs410121	0.92[EUR][1000 genomes]
rs411413	0.89[EUR][1000 genomes]
rs412039	0.90[EUR][1000 genomes]
rs414499	0.89[EUR][1000 genomes]
rs415676	0.88[EUR][1000 genomes]
rs416228	0.89[EUR][1000 genomes]
rs420122	0.90[EUR][1000 genomes]
rs421030	0.90[EUR][1000 genomes]
rs423651	0.89[EUR][1000 genomes]
rs431519	0.92[EUR][1000 genomes]
rs431562	0.90[EUR][1000 genomes]
rs437662	0.90[EUR][1000 genomes]
rs437906	0.89[EUR][1000 genomes]
rs438762	0.90[EUR][1000 genomes]
rs438966	0.92[EUR][1000 genomes]
rs439310	0.92[EUR][1000 genomes]
rs444650	0.89[EUR][1000 genomes]
rs447476	0.90[EUR][1000 genomes]
rs448287	0.90[EUR][1000 genomes]
rs449472	0.89[EUR][1000 genomes]
rs450194	0.92[EUR][1000 genomes]
rs450286	0.90[EUR][1000 genomes]
rs450643	0.90[EUR][1000 genomes]
rs451045	0.92[EUR][1000 genomes]
rs452789	0.89[EUR][1000 genomes]
rs453568	0.90[EUR][1000 genomes]
rs453933	0.90[EUR][1000 genomes]
rs454269	0.90[EUR][1000 genomes]
rs4668654	0.88[AFR][1000 genomes]
rs4669497	0.88[AFR][1000 genomes]
rs4669498	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669499	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669500	0.89[AFR][1000 genomes]
rs499858	0.92[EUR][1000 genomes]
rs55664551	0.88[AFR][1000 genomes]
rs56010640	0.92[EUR][1000 genomes]
rs56258032	0.83[EUR][1000 genomes]
rs56382546	0.84[EUR][1000 genomes]
rs58979565	0.90[AFR][1000 genomes]
rs62127468	0.88[AFR][1000 genomes]
rs71437684	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9750736	0.84[AFR][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	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1005938	chr2:10043181-10074384	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS 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	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs56241824	TAF1B	cis	Nerve Tibial	GTEx
rs56241824	TAF1B	cis	Artery Tibial	GTEx
rs56241824	TAF1B	cis	Adipose Subcutaneous	GTEx
rs56241824	TAF1B	Cis_1M	lymphoblastoid	RTeQTL
rs56241824	TAF1B	cis	Muscle Skeletal	GTEx
rs56241824	RP11-95D17.1	cis	Adipose Subcutaneous	GTEx
rs56241824	TAF1B	cis	Esophagus Muscularis	GTEx
rs56241824	RP11-95D17.1	cis	Skin Sun Exposed Lower leg	GTEx
rs56241824	TAF1B	cis	Skin Sun Exposed Lower leg	GTEx
rs56241824	TAF1B	cis	lung	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9993800-10079600	Weak transcription	Gastric	stomach
2	chr2:10017800-10073000	Weak transcription	Right Ventricle	heart
3	chr2:10026000-10072800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:10030400-10077200	Weak transcription	Aorta	Aorta
5	chr2:10030600-10080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:10036600-10076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:10036800-10073000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:10037200-10080400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:10037800-10075600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:10038600-10079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:10038600-10081400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:10042600-10077000	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:10045800-10079600	Weak transcription	Esophagus	oesophagus
14	chr2:10046000-10075200	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:10047200-10080000	Weak transcription	Colonic Mucosa	Colon
16	chr2:10049000-10077400	Weak transcription	Brain Anterior Caudate	brain
17	chr2:10049400-10077200	Weak transcription	Brain Angular Gyrus	brain
18	chr2:10049400-10081000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:10049600-10081200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:10052800-10076600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:10053200-10077800	Weak transcription	Liver	Liver
22	chr2:10054600-10073400	Weak transcription	Brain Substantia Nigra	brain
23	chr2:10054800-10072200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:10054800-10079000	Weak transcription	Fetal Kidney	kidney
25	chr2:10055000-10072600	Weak transcription	Spleen	Spleen
26	chr2:10055000-10080800	Weak transcription	Pancreas	Pancrea
27	chr2:10055000-10080800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:10055000-10081800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:10055200-10072600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:10055200-10072800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:10055200-10073200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr2:10055200-10079600	Weak transcription	K562	blood
33	chr2:10055200-10080800	Weak transcription	HMEC	breast
34	chr2:10055600-10073000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:10055800-10075800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr2:10056800-10074200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:10058800-10076000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:10059000-10080600	Weak transcription	HSMMtube	muscle
39	chr2:10059200-10072800	Weak transcription	Left Ventricle	heart
40	chr2:10059400-10081200	Weak transcription	GM12878-XiMat	blood
41	chr2:10059600-10072600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr2:10060000-10073400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:10060200-10071200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:10060400-10073000	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr2:10060400-10075800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr2:10060600-10072800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:10060600-10072800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:10060600-10073200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:10060600-10073200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:10060600-10073400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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