Variant report

Variant	rs71543775
Chromosome Location	chr7:56073670-56073671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:56073380..56075389-chr7:56117941..56120031,2	MCF-7	breast:
2	chr7:56072684..56074184-chr7:56076449..56078761,2	K562	blood:

Variant related genes	Relation type
ENSG00000146731	Chromatin interaction
ENSG00000146733	Chromatin interaction

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];0.83[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];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34334997	0.92[ASN][1000 genomes]
rs34477367	1.00[AFR][1000 genomes];0.83[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];0.85[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	0.82[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];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71543776	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71543777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[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
rs71543775	GBAS	cis	Thyroid	GTEx

Chromatin state (count:109 , 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	chr7:56051800-56077000	Weak transcription	NHEK	skin
7	chr7:56053000-56074200	Weak transcription	Hela-S3	cervix
8	chr7:56053000-56078200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:56058400-56077800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:56060600-56099600	Weak transcription	HUVEC	blood vessel
11	chr7:56063200-56077800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr7:56063400-56089600	Weak transcription	NHDF-Ad	bronchial
13	chr7:56063400-56096800	Weak transcription	NH-A	brain
14	chr7:56063600-56079800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr7:56063600-56101000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:56063600-56101200	Weak transcription	NHLF	lung
17	chr7:56064000-56078200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr7:56064200-56076600	Weak transcription	HMEC	breast
19	chr7:56064200-56079600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:56064400-56087200	Weak transcription	Aorta	Aorta
21	chr7:56064400-56087200	Weak transcription	Esophagus	oesophagus
22	chr7:56064400-56101400	Weak transcription	Gastric	stomach
23	chr7:56064600-56074400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr7:56064600-56074800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr7:56064600-56075000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr7:56064600-56078200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:56064800-56078600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:56065000-56081000	Weak transcription	HSMMtube	muscle
29	chr7:56065000-56081600	Weak transcription	Fetal Thymus	thymus
30	chr7:56065000-56101400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr7:56065000-56101400	Weak transcription	Colonic Mucosa	Colon
32	chr7:56065200-56075600	Weak transcription	Brain Angular Gyrus	brain
33	chr7:56065400-56075000	Weak transcription	Brain Substantia Nigra	brain
34	chr7:56065400-56078200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr7:56065400-56101400	Weak transcription	Fetal Brain Male	brain
36	chr7:56065800-56075200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr7:56065800-56076600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr7:56065800-56077000	Weak transcription	Pancreas	Pancrea
39	chr7:56065800-56077400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr7:56065800-56078400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:56065800-56088400	Weak transcription	Fetal Kidney	kidney
42	chr7:56065800-56095800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr7:56066000-56078600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr7:56066200-56086600	Weak transcription	Ovary	ovary
45	chr7:56066600-56074000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr7:56066600-56079200	Weak transcription	A549	lung
47	chr7:56066600-56087400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr7:56066800-56074000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr7:56066800-56075000	Weak transcription	Brain Anterior Caudate	brain
50	chr7:56066800-56077800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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