Variant report

Variant	rs538103
Chromosome Location	chr11:74072173-74072174
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1044782	0.89[ASN][1000 genomes]
rs1053021	0.89[ASN][1000 genomes]
rs10736795	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10793072	0.89[ASN][1000 genomes]
rs10793073	0.89[ASN][1000 genomes]
rs10793074	0.89[ASN][1000 genomes]
rs10793075	0.89[ASN][1000 genomes]
rs10793078	0.84[ASN][1000 genomes]
rs10793079	0.93[ASN][1000 genomes]
rs10793080	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10793081	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10898981	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10898983	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11236061	0.89[ASN][1000 genomes]
rs11236068	0.93[ASN][1000 genomes]
rs11236073	0.86[ASN][1000 genomes]
rs11236087	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11236088	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1145687	0.85[ASN][1000 genomes]
rs11559629	0.91[ASN][1000 genomes]
rs2887119	0.91[ASN][1000 genomes]
rs3168173	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35170680	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3741130	0.89[ASN][1000 genomes]
rs3862799	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3867268	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3867270	0.89[ASN][1000 genomes]
rs3867271	0.93[ASN][1000 genomes]
rs3867272	0.93[ASN][1000 genomes]
rs479968	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs480358	0.93[ASN][1000 genomes]
rs486758	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944041	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4944887	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs519083	0.89[ASN][1000 genomes]
rs563626	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs58950228	0.90[ASN][1000 genomes]
rs592644	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs595798	0.89[ASN][1000 genomes]
rs596976	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597729	0.93[ASN][1000 genomes]
rs598869	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61902399	0.85[ASN][1000 genomes]
rs623065	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625632	0.89[ASN][1000 genomes]
rs634608	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs637921	0.89[ASN][1000 genomes]
rs641271	0.89[ASN][1000 genomes]
rs646047	0.93[ASN][1000 genomes]
rs655719	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs657329	0.93[ASN][1000 genomes]
rs6592557	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs662393	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs673103	0.93[ASN][1000 genomes]
rs7120394	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7926851	0.89[ASN][1000 genomes]
rs7928036	0.89[ASN][1000 genomes]
rs7930193	0.86[ASN][1000 genomes]
rs7934621	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7940145	0.93[ASN][1000 genomes]
rs7941916	0.89[ASN][1000 genomes]
rs7944333	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7945908	0.93[ASN][1000 genomes]
rs7947911	0.86[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	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv1049915	chr11:74052264-74126319	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs538103	HNRNPA1P40	cis	Thyroid	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74037400-74078800	Weak transcription	Small Intestine	intestine
2	chr11:74037800-74086200	Weak transcription	Brain Anterior Caudate	brain
3	chr11:74038000-74077400	Weak transcription	Psoas Muscle	Psoas
4	chr11:74038000-74077600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:74038000-74084400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr11:74038200-74082000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:74038200-74084400	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:74038400-74084400	Weak transcription	Liver	Liver
9	chr11:74038400-74086200	Weak transcription	Adipose Nuclei	Adipose
10	chr11:74042000-74077600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr11:74042200-74081200	Weak transcription	Hela-S3	cervix
12	chr11:74044800-74079200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr11:74045800-74073200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:74047800-74077600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr11:74048400-74077800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:74049400-74080400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr11:74049800-74077400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr11:74050800-74085800	Weak transcription	Colonic Mucosa	Colon
19	chr11:74056600-74077600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:74056800-74077400	Weak transcription	HSMMtube	muscle
21	chr11:74059000-74077600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:74062800-74077600	Weak transcription	HUVEC	blood vessel
23	chr11:74066000-74077600	Weak transcription	NH-A	brain
24	chr11:74067200-74072400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr11:74068600-74072800	Strong transcription	Fetal Brain Female	brain
26	chr11:74068800-74094800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr11:74069000-74077400	Weak transcription	HSMM	muscle
28	chr11:74069400-74082800	Weak transcription	Fetal Kidney	kidney
29	chr11:74069600-74077600	Weak transcription	A549	lung
30	chr11:74070000-74072200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr11:74070400-74072400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr11:74070400-74072800	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr11:74070400-74072800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr11:74070600-74072800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
35	chr11:74070800-74072200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
36	chr11:74070800-74072200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:74070800-74072800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr11:74070800-74072800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
39	chr11:74070800-74072800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
40	chr11:74070800-74072800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr11:74070800-74072800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
42	chr11:74071000-74072200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
43	chr11:74071000-74072200	ZNF genes & repeats	Fetal Intestine Large	intestine
44	chr11:74071000-74072200	ZNF genes & repeats	Fetal Intestine Small	intestine
45	chr11:74071000-74072400	ZNF genes & repeats	Fetal Stomach	stomach
46	chr11:74071000-74072800	Strong transcription	Primary T cells from cord blood	blood
47	chr11:74071000-74083000	Weak transcription	Brain Hippocampus Middle	brain
48	chr11:74071200-74072200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:74071200-74072200	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr11:74071200-74072200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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