Variant report

Variant	rs16961703
Chromosome Location	chr17:63240344-63240345
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	chr17:63223927..63226638-chr17:63237839..63240467,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11079561	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658673	0.80[CEU][hapmap]
rs11658773	0.80[CEU][hapmap]
rs16960903	0.92[MEX][hapmap]
rs16960957	0.80[CEU][hapmap]
rs16961727	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961732	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961868	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16961878	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961897	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17689671	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28476544	1.00[ASN][1000 genomes]
rs28895913	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791220	0.85[CEU][hapmap]
rs55820790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55853855	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56202104	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56205487	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56408543	1.00[ASN][1000 genomes]
rs56684368	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57333496	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58012124	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58931966	0.83[EUR][1000 genomes]
rs60495439	1.00[ASN][1000 genomes]
rs60919543	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62063085	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62063086	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62065142	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62065143	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62065144	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62065147	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6504287	0.86[EUR][1000 genomes]
rs6504288	0.84[EUR][1000 genomes]
rs67111745	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207480	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207744	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7211786	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7212442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215623	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219197	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219498	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219691	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7220948	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221258	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221276	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221428	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7221810	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72845315	0.86[ASN][1000 genomes]
rs72854623	0.86[ASN][1000 genomes]
rs7342966	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065208	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8071511	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072237	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074052	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077032	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077396	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8078209	1.00[ASN][1000 genomes]
rs8078293	0.89[CEU][hapmap]
rs8078535	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078847	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080929	0.85[CEU][hapmap];0.92[MEX][hapmap]
rs8081224	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8082275	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8082401	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889653	0.80[CEU][hapmap]
rs9896491	0.84[EUR][1000 genomes]
rs9897086	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897299	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898094	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905007	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9905226	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9909786	1.00[CHB][hapmap]
rs9914176	1.00[ASN][1000 genomes]
rs9916525	0.95[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530764	chr17:62939944-63278472	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv482610	chr17:63214370-63372334	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16961703	TBX2	cis	parietal	SCAN
rs16961703	CA4	cis	parietal	SCAN
rs16961703	GDPD1	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:63239600-63241000	Enhancers	Fetal Brain Male	brain
2	chr17:63239600-63241200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr17:63239800-63240400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr17:63239800-63240400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr17:63239800-63240400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr17:63239800-63240400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr17:63239800-63240400	Enhancers	Brain Angular Gyrus	brain
8	chr17:63239800-63240400	Enhancers	Brain Hippocampus Middle	brain
9	chr17:63239800-63240400	Enhancers	Brain Substantia Nigra	brain
10	chr17:63239800-63240600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:63239800-63240600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr17:63239800-63240600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr17:63239800-63240600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr17:63239800-63240600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr17:63239800-63240600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:63239800-63240600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr17:63239800-63240600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr17:63239800-63240600	Enhancers	Brain Anterior Caudate	brain
19	chr17:63239800-63240600	Enhancers	Brain Cingulate Gyrus	brain
20	chr17:63239800-63240600	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr17:63239800-63240600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr17:63239800-63240600	Enhancers	Fetal Stomach	stomach
23	chr17:63239800-63240800	Enhancers	H1 Cell Line	embryonic stem cell
24	chr17:63239800-63240800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr17:63239800-63240800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr17:63240000-63240400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr17:63240000-63240400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:63240000-63240400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr17:63240000-63240400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr17:63240000-63240400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
31	chr17:63240000-63240400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
32	chr17:63240000-63240400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr17:63240000-63240400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr17:63240000-63240400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr17:63240000-63240400	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr17:63240000-63240400	Enhancers	Colon Smooth Muscle	Colon
37	chr17:63240000-63240400	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr17:63240000-63240400	Enhancers	Esophagus	oesophagus
39	chr17:63240000-63240400	Enhancers	Fetal Lung	lung
40	chr17:63240000-63240400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr17:63240000-63240400	Enhancers	Placenta Amnion	Placenta Amnion
42	chr17:63240000-63240400	Enhancers	Rectal Smooth Muscle	rectum
43	chr17:63240000-63240600	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr17:63240000-63240600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr17:63240000-63240600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr17:63240000-63240600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
47	chr17:63240000-63240600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr17:63240000-63240600	Flanking Active TSS	Fetal Brain Female	brain
49	chr17:63240000-63240600	Enhancers	Fetal Thymus	thymus
50	chr17:63240000-63240600	Bivalent Enhancer	HSMM	muscle

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