Variant report

Variant	rs71543777
Chromosome Location	chr7:56080240-56080241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10085802	0.92[ASN][1000 genomes]
rs10253539	0.92[ASN][1000 genomes]
rs10253680	0.92[ASN][1000 genomes]
rs12555	0.92[ASN][1000 genomes]
rs13223519	1.00[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13228321	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13229704	0.92[ASN][1000 genomes]
rs13233834	0.92[ASN][1000 genomes]
rs13234504	0.92[ASN][1000 genomes]
rs13240361	0.92[ASN][1000 genomes]
rs13241531	0.92[ASN][1000 genomes]
rs13247558	0.92[ASN][1000 genomes]
rs17151447	0.92[ASN][1000 genomes]
rs2304375	0.92[ASN][1000 genomes]
rs2331184	0.92[ASN][1000 genomes]
rs33922584	0.92[ASN][1000 genomes]
rs34154824	0.92[ASN][1000 genomes]
rs34319969	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34334997	0.92[ASN][1000 genomes]
rs34477367	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs34822782	0.92[ASN][1000 genomes]
rs35007015	0.92[ASN][1000 genomes]
rs35058595	0.92[ASN][1000 genomes]
rs35136814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35347055	0.92[ASN][1000 genomes]
rs35506072	0.92[ASN][1000 genomes]
rs35515485	0.92[ASN][1000 genomes]
rs35523043	0.92[ASN][1000 genomes]
rs35581685	0.92[ASN][1000 genomes]
rs35818005	0.86[ASN][1000 genomes]
rs35881493	0.92[ASN][1000 genomes]
rs36044787	0.92[ASN][1000 genomes]
rs36049923	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36148650	0.92[ASN][1000 genomes]
rs3778868	0.92[ASN][1000 genomes]
rs4947527	0.86[ASN][1000 genomes]
rs4947531	0.89[ASN][1000 genomes]
rs4948089	0.89[ASN][1000 genomes]
rs4948101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71543775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71543776	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73126344	0.92[ASN][1000 genomes]
rs816242	0.89[ASN][1000 genomes]
rs816412	0.92[ASN][1000 genomes]
rs816413	0.92[ASN][1000 genomes]
rs816415	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers 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	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats 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	84 gene(s)	inside rSNPs	diseases
5	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS 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 target site	46 gene(s)	inside rSNPs	diseases
6	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
9	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
12	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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	27 gene(s)	inside rSNPs	diseases
14	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv1017793	chr7:56051267-56098030	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs71543777	GBAS	cis	Thyroid	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56033200-56081400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:56039200-56081600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:56049200-56101600	Weak transcription	Small Intestine	intestine
4	chr7:56050000-56086600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:56051400-56086800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:56060600-56099600	Weak transcription	HUVEC	blood vessel
7	chr7:56063400-56089600	Weak transcription	NHDF-Ad	bronchial
8	chr7:56063400-56096800	Weak transcription	NH-A	brain
9	chr7:56063600-56101000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr7:56063600-56101200	Weak transcription	NHLF	lung
11	chr7:56064400-56087200	Weak transcription	Aorta	Aorta
12	chr7:56064400-56087200	Weak transcription	Esophagus	oesophagus
13	chr7:56064400-56101400	Weak transcription	Gastric	stomach
14	chr7:56065000-56081000	Weak transcription	HSMMtube	muscle
15	chr7:56065000-56081600	Weak transcription	Fetal Thymus	thymus
16	chr7:56065000-56101400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr7:56065000-56101400	Weak transcription	Colonic Mucosa	Colon
18	chr7:56065400-56101400	Weak transcription	Fetal Brain Male	brain
19	chr7:56065800-56088400	Weak transcription	Fetal Kidney	kidney
20	chr7:56065800-56095800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr7:56066200-56086600	Weak transcription	Ovary	ovary
22	chr7:56066600-56087400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr7:56066800-56086000	Weak transcription	Brain Germinal Matrix	brain
24	chr7:56067000-56080400	Weak transcription	Thymus	Thymus
25	chr7:56067000-56080800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:56067000-56081400	Weak transcription	Osteobl	bone
27	chr7:56067000-56082200	Weak transcription	Lung	lung
28	chr7:56067000-56088600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr7:56067200-56087000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr7:56067200-56101400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr7:56067400-56081000	Weak transcription	HSMM	muscle
32	chr7:56067400-56087200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr7:56067400-56087600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr7:56067400-56100800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr7:56067800-56099600	Weak transcription	K562	blood
36	chr7:56068200-56080800	Weak transcription	Placenta	Placenta
37	chr7:56068200-56081000	Weak transcription	Fetal Lung	lung
38	chr7:56068200-56081000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr7:56068200-56081000	Weak transcription	GM12878-XiMat	blood
40	chr7:56068200-56081200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:56068200-56081200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:56068200-56086200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr7:56068200-56087400	Weak transcription	Adipose Nuclei	Adipose
44	chr7:56068200-56101200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr7:56068400-56081000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr7:56068400-56081000	Weak transcription	Primary T cells from cord blood	blood
47	chr7:56068400-56081000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr7:56068400-56081600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr7:56068400-56087200	Weak transcription	Fetal Brain Female	brain
50	chr7:56072800-56087400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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